bluuebunny/crossref_metadata_2025 huggingface dataset:
Metabolism and the biochemistry of glucose
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

This chapter describes the nature of chemical energy within cells and looks at how this energy is harnessed from enzyme-catalysed reactions. It deals with the relation of cellular energy to the ability to facilitate dehydration chemistry in aqueous solution and the primary source of dehydrating power in cells. It also analyses the establishment of the nature of biochemical energy and explains how the biochemistry of glucose is used as an example of the manipulation of chemicals in cells. The chapter mentions mechanical, electrical, and chemical energies, which are the forms of energy cells use. It also discusses constructed polymers, which are characteristic of life. The polymers common to all living systems correspond to the joining of monomer units with concomitant loss of water.
Geneticinformation: nucleotides and nucleic acids
Authors: Dobson C. M. , Gerrard J.A. , Pratt A.J.
Published: September 2023

This chapter discusses the nature of nucleotides and the polymers that derive from nucleotides called nucleic acids, demonstrating how they fold into ordered structures and give rise to the spontaneous assembly of lipids into membranes. It illustrates the structural features of nucleic acids that are exploited in their role as information stores. It also outlines cells as complex entities and localized capsules of chemicals that can reproduce to generate new cells of a near-identical nature. The chapter highlights that the nature of a particular cell depends on the array of chemicals within the cell and the nature of their interconversion. It analyses how proteins are involved in all activities of the cell, such as the uptake and transport of small molecules and the catalysis of chemical reactions.
Nucleophilic substitution at C=O with loss of carbonyl oxygen
Authors: Clayden Jonathan , Greeves Nick , Warren Stuart
Published: September 2023

This chapter explores nucleophilic substitution at the carbonyl group with loss of carbonyl oxygen. It looks at two important examples: the carbonyl oxygen atom has been replaced by a nitrogen atom during imine formation and by two atoms of oxygen during acetal formation. When acetaldehyde is dissolved in methanol, a reaction takes place; the product is a hemiacetal. Like hydrates, most hemiacetals are unstable with respect to their parent aldehydes and alcohols. The chapter then considers how acetals are formed from aldehydes or ketones plus alcohols in the presence of acid. In the presence of acid, hemiacetals can undergo an elimination reaction, losing the oxygen atom that once belonged to the parent aldehyde’s carbonyl group.
The Evolution of Plants
Authors: Willis K. J. , McElwain J. C.
Published: September 2023

The Evolution of Plants examines evolutionary recording and methods of reconstruction of plant life. It also discusses the earliest forms of plant life, the colonization of land, the first forests, and the major emergence of the seed plants. Other chapters look at flowering plant origins, the past 65 million years, and the mass extinctions and persistent populations. Towards the end, the text looks at ancient DNA and the biomolecular record, as well as evolutionary theories and the plant fossil record.
Molecular Quantum Mechanics
Authors: Atkins Peter , Friedman Ronald
Published: September 2023

Molecular Quantum Mechanics shows how the subject of quantum mechanics embraces the behaviour of all known forms of matter, including the atoms and molecules from which we, and all living organisms, are composed. The book leads us through this subject, exploring the fundamental physical principles that explain how all matter behaves. The text takes us from the foundations of quantum mechanics, through quantum models of atomic, molecular, and electronic structure, and on to discussions of spectroscopy, and the electronic and magnetic properties of molecules.
Quantum mechanics and spectroscopy
Authors: Keeler James , Wothers Peter
Published: September 2023

This chapter addresses quantum mechanics and spectroscopy. Two key ideas emerge from the theory of quantum mechanics: the first is that the electron is described by a wavefunction, and the second is that the energy of the electron is quantized. The wavefunction is important since its square gives the probability density of the electron. Quantization means that the energy can only have certain discrete values, rather than being allowed to vary continuously. The chapter looks at how these wavefunctions and energy levels arise in quantum mechanics, and how they can actually be computed in some simple cases. This will involve setting up and then solving the famous Schrödinger equation. Quantum mechanics is not restricted to the description of electrons in atoms and molecules, but can also be used to describe the motion of molecules in space (translation), as well as the rotation and vibration of molecules.
Arithmetic and algebra
Authors: Reed Martin B
Published: September 2023

This chapter gives an abstract approach that builds up the rules from basic concepts of real numbers and arithmetic operations. It presents mathematics in a bioscience context and includes case studies that show how a range of different mathematical techniques are needed in the development of a biological topic. It also introduces geometric growth, which is used to model colonies of certain populations in situations where the birth rate exceeds the mortality rate, there are sufficient supplies of food, and there is an absence of predators or diseases. The chapter describes a mathematical model that expresses the rates of change of the densities of the three types of cell: healthy, stage one cancer, and angiogenic cells. It examines the evaluation of numerical expressions and algebraic expressions involving fractions, exponents, and roots.
Is sex good for survival?
Authors: Bromham Lindell , Cardillo Marcel
Published: September 2023

This chapter addresses the evolution of sex. Sex results in offspring with DNA from more than one parent. Sexual reproduction is so common and familiar that it may come as a surprise to find that it has been an enduring puzzle in evolutionary biology. Given that many species can reproduce uniparentally, without needing to combine genes with other individuals, why would sex evolve? And given that asexual lineages frequently evolve from sexual species, why do so many different species retain sexual reproduction? Many different solutions have been proposed for both the origin and maintenance of sexual reproduction, ranging from genome repair to long-term evolvability. This broad range of proposed mechanisms requires us to think about how evolution works at different levels of biological organization, from ‘selfish genes’ to evolutionary lineages, and at different timescales, from individual lifetimes to millions of years.
Viruses
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter concentrates on the basic biology of viruses. It begins by describing a number of features of viruses, then it demonstrates the organization of a typical virus particle. The chapter examines the way in which viruses replicate themselves from virus to virus. It also presents the remarkable feature of most viruses: the symmetrical structure of their protein coat. The chapter then shifts to explain the specific receptor of each virus, usually a vital component of the cell surface. It also discusses the several effects of infection of a cell by a virus. Next, the chapter illustrates some key dates in the gradual unfolding of the viruscancer link. It also looks at the main routes of viral spread and the introduction of vaccines.
Bacteria
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter focuses on a discussion about bacteria. It begins by looking at one part of the bacterium with a special significance for both disease and immunity: the cell wall. By providing information on bacterial classification, the chapter illustrates three types of bacterial cell wall which vary greatly in their structure: the gram-positive, mycobacterium, and the gram-negative. The chapter then moves to describe parasitic bacteria and makes a distinction between aerobic and anaerobic bacteria in certain infections. It also examines bacteria which do not fit neatly into classification. Next, the chapter examines bacterial replication, emphasizing the special features of gene expression and the method for bringing about rapid changes in genes: phase variation. The chapter also talks about the control of bacterial disease by antibiotics and the remarkable number of ways in which bacteria, far from being pathogenic, are useful and even essential to humans and animals.
Fungi
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter looks at the structure and morphology of fungi. It begins with considering the distinction of the basic cell design and plasma membrane of fungi and humans. The chapter then examines the fungi which grow on skin, nails, and hair, known collectively as dermatophytes. The chapter further examines cutaneous and superficial mycoses, subcutaneous mycoses, and systemic mycoses. The chapter also demonstrates that fungal infections are not easily controlled, but there are some quite effective antifungal drugs. Finally, the chapter looks at the beneficial side of fungi, highlighting yeasts as an obvious example. It notes that yeasts, recently, have proved to be good cells in which to insert foreign genes so as to manufacture large amounts of a pure protein.
The antibody response
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter examines how B-cells and T-cells, acting together, give rise to the production of antibody molecules: the antibody response. It begins with discussing the activation of B-cells, which occurs mainly in the lymphoid organs (the site depending on the route by which antigen arrives). The chapter then looks at the different sorts of antigen to activate B-cells in different ways, emphasizing the T-independent (Ti antigens) and T-dependent (TD). It then shifts to investigate how an immunoglobulin molecule on the surface of the B-cell switches on the intracellular mechanisms that lead to antibody formation. Next, the chapter outlines the consequences of the activation through the B-cell antigenreceptor complex. It also looks at the signals of T-cell activation, then reviews the B-cell memory and the antibody responses at mucosal surfaces.
How pathogens escape adaptive immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter stresses that every pathogen has its own approach to the problem of being recognized by B and T-cells. It begins by describing the attempts to conceal the presence of pathogen from lymphocytes. Anything that intervenes between a microbial antigen and a B or T-cell capable of recognizing it will obviously reduce the chances of inducing an immune response, or of restimulating already existing memory cells. It then presents the three fairly common things that can do this: cell membranes, cysts, and host-derived molecules taken up by the pathogen. The chapter also elaborates on the antigenic variation, one of the most cunning of all pathogen strategies, highly effective at confusing the recognition systems of adaptive immunity. Finally, it explores the suppression or modulation of lymphocytes or lymphocyte function. It then gives some examples of immunosuppression, and considers pregnancy, transplants, and tumours.
Disease due to adaptive immunity II: autoimmunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter discusses the underlying causes of autoimmunity, focusing on infection and genetic predisposition. It seeks to understand how autoimmunity is normally avoided, and why do some B and T lymphocytes do not recognize and respond to 'self' antigens, considering that their receptors are produced by a random recombination of genes and should be able to recognize virtually everything, instead of being unresponsive, or tolerant, to self. The chapter begins by analyzing the polyclonal activation of anti-self B or T lymphocytes. It then looks into the activation of T lymphocytes by antigens closely similar to self: molecular mimicry. The chapter then shifts to detail the release of sequestered antigens, and displays one of the striking findings in organs affected by autoimmunity, the appearance of MHC class II antigens on cells where they are normally absent. Finally, the chapter reviews the anomalous cytokine production, autoimmune disease, and genetics.
Immunodeficiency II: primary defects of adaptive immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter recalls the difference between primary (genetic) and secondary (acquired) immunodeficiency affecting the adaptive immune system. It emphasizes that the primary adaptive immunodeficiencies are inherited, so that they are either X-linked or autosomal. The chapter then jumps to illustrate the defects affecting T-cells, B-cells, and antibody. It also demonstrates the clinical aspects of primary immune deficiencies, arguing that primary immune deficiencies represent one of the best opportunities for immunological principles to be applied to human disease. Next, the chapter brings up the specialist centres where diagnosis and treatment can be carried out. It also investigates the nature of haemopoietic stem cells and gene therapy.
Epidemiology
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter considers the balance between human populations and their pathogens with two crucial aims: to understand the 'real world' situation, and where necessary, to try and control it. It delves into some of the factors that determine the incidence and distribution of infectious diseases; that is, their epidemiology. The chapter begins by describing the diagnosis, which can be clinical, microbiological, or immunological. It explains the theoretical epidemiology and practical epidemiology, then highlights four main factors, all of which need to be understood by those working in the 'real world': the host and its variables; the pathogen and its variables; the degree of contact between the two; and the effect, if any, of treatment or preventive measures. The chapter illustrates these points in relation to three diseases, one viral (AIDS), one bacterial (tuberculosis), and one protozoal (malaria). Ultimately, the chapter considers infantile diarrhoea, then reviews the value of epidemiology.
Control of infectious disease: vaccination
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter uncovers how immunization makes use of the ability of the adaptive immune system to learn and improve. It argues that immunization may be active, inducing the immune system itself to acquire a permanently enhanced resistance to a particular pathogen, or passive, where a preformed antibody is introduced into the individual to be protected. Active immunization directed at a specific organism is known as vaccination. The chapter then explores the function and aim of a vaccine. It begins by explicating the four requirements of a vaccine: effective, safe, stable, and affordable. The chapter also demonstrates some established and some still experimental vaccines. For practical purposes, the essential distinction is between living and non-living vaccines. Finally, the chapter tracks other vaccine strategies and the development of a new vaccine. It also considers the passive ('immediate') immunization and therapeutic vaccines.
Control of infectious disease: chemotherapy
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter examines the idea of using chemicals safely to attack microbes. It presents chemical substances which are used at four levels to kill pathogens: disinfectants, antiseptics, chemotherapy, and antibiotics. The chapter then shows that chemotherapy has been extremely successful against many bacteria, because their procaryotic structure offers several targets absent from eucaryotic cells. The chapter also elaborates on some antibacterial agents, highlighting the modern antibacterials such as the synthetic azo-dye sulphanilamide, the true antibiotics penicillin, and streptomycin. The chapter then shifts to investigate how antibiotic resistance can develop at several levels. It looks at the standard susceptibility test, biofilm, and bacterial interference. Next, the chapter analyzes the other problem with antibiotics, as with all drugs: toxicity. It then displays some of the effective drugs against eucaryotic infections.
Viral and prion disease and immunity
Authors: Playfair John H.L. , Bancroft Gregory J.
Published: September 2023

This chapter surveys the individual features of the principal virus infections, considered from a clinical, pathological, and immunological viewpoint. It discusses some common childhood viruses such as measles, rubella, mumps, chickenpox, and skin rashes. Measles, rubella, and chickenpox are similar in being spread by the respiratory route and infecting a high proportion of contacts, measles especially, with prominent skin lesions. The chapter also examines the causes of common colds induced by a variety of viruses. It looks at the viruses affecting the nose and throat. The chapter then shifts to expound on other enteroviruses and herpesviruses, then considers viral hepatitis, rabies, and other viral zoonoses. It concludes by talking about yellow fever and dengue, papillomaviruses, and prion diseases.
Differential equations
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

A differential equation is a relation between a function and its derivatives, as in

where f is a function of the variable x and...
Translational motion in several dimensions
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Motion in two dimensions 87

Separation of variables 88

Brief illustration 11.1: The zero-point energy of a particle in a two-dimensional box 89

Brief illustration 11.2: The distribution of a particle in a two-dimensional box 89

Degeneracy 89

Brief illustration 11.3:...
Matrices
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

A matrix is an array of numbers that are generalizations of ordinary numbers. We shall consider only square matrices, which have the numbers arranged in the same number of rows and columns. By using matrices, we can manipulate large numbers of ordinary numbers simultaneously. A...
Fourier series and Fourier transforms
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Some of the most versatile mathematical functions are the trigonometric functions sine and cosine. As a result, it is often very helpful to express a general function as a linear combination of these functions and then to carry out manipulations on the resulting series. Because...
Rotational spectroscopy
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Microwave spectroscopy 396

Selection rules 396

Brief illustration 42.1: Gross selection rules for microwave spectroscopy 397

The appearance of microwave spectra 398

Example 42.1: Predicting the appearance of a rotational spectrum 398

Rotational Raman spectroscopy 399

Example 42.2: Predicting the...
Vibrational spectroscopy: polyatomic molecules
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Normal modes 415

Brief illustration 44.1: The numbers of normal modes 416

Infrared absorption spectra of polyatomic molecules 417

Example 44.1: Using the gross selection rule for infrared spectroscopy 417

Example 44.2: Interpreting an infrared spectrum 418

Vibrational Raman spectra of...
The Boltzmann distribution
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Configurations and weights 499

Instantaneous configurations 499

Brief illustration 51.1: The weight of a configuration 499

The most probable distribution 500

Brief illustration 51.2: The Boltzmann distribution 501

The relative population of states 501

Example 51.1: Calculating the relative populations...
Molecular partition functions
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The significance of the partition function 506

Brief illustration 52.1: A partition function 507

Contributions to the partition function 508

The translational contribution 509

Brief illustration 52.2: The translational partition function 510

The rotational contribution 510

Example 52.1: Evaluating the...
Molecular energies
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The basic equations 517

Brief illustration 53.1: Mean energy of a two-level system 518

The translational contribution 518

Brief illustration 53.2: The equipartition theorem 519

The rotational contribution 519

Brief illustration 53.3: Mean rotational energy 520

The vibrational contribution...
Ideal mixtures
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The mixing of perfect gases 679

Example 70.1: Calculating a Gibbs energy of mixing 680

The mixing of liquids 682

Raoult’s law 682

Brief illustration 70.1: Raoult’s law 683

Henry’s law 684

Example 70.2: Investigating the validity of Raoult’s and...
Integrated rate laws
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

First-order reactions 806

Example 83.1: Analysing a first-order reaction 807

Second-order reactions 808

Brief illustration 83.1: Second-order reactions 809

Checklist of concepts 811

Checklist of equations 811

Why do you need to know this material?

A complete analysis of the time...
The Arrhenius equation
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

The temperature dependence of reaction rates 816

Example 85.1: Determining the Arrhenius parameters 817

Brief illustration 85.1: The Arrhenius equation 817

The interpretation of the Arrhenius parameters 818

A first look at the energy requirements of reactions 818

Brief illustration 85.2:...
Diffusion-controlled reactions
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Reaction in solution 843

Classes of reaction 843

Diffusion and reaction 844

Brief illustration 88.1: Diffusion control 1 844

Brief illustration 88.2: Diffusion control 2 845

The material-balance equation 845

The formulation of the equation 846

Solutions of...
Enzymes
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Features of enzymes 881

The Michaelis–Menten mechanism 882

Example 92.1: Analysing a Lineweaver–Burk plot 883

The catalytic efficiency of enzymes 884

Brief illustration 92.1: The catalytic efficiency of an enzyme 885

Mechanisms of enzyme inhibition 885

Example 92.2: Distinguishing between...
Solid surfaces
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Surface growth 912

The collision flux 913

Physisorption and chemisorption 913

Fractional coverage 914

Experimental techniques 914

Microscopy 915

Ionization techniques 916 Brief illustration 95.3: A UPS spectrum 916 Brief illustration 95.4:...
Heterogeneous catalysis
Authors: Atkins Peter , de Paula Julio , Friedman Ronald
Published: September 2023

Contents

Mechanisms of heterogeneous catalysis 931

Unimolecular reactions 932

Surface-catalysed unimolecular decomposition 932

The Langmuir-Hinshelwood mechanism 932

Writing a rate law based on the Langmuir-Hinshelwood mechanism 932

The Eley–Rideal mechanism 933

The Eley–Rideal...
Calorimetry
Authors: Campbell Iain D.
Published: September 2023

Introduction

Calorimetry (Latin calor = heat) measures the heat produced by chemical reactions or physical changes. Joseph Black (1728–1799) is usually said to be the founder of the method but Antoine Lavoisier (1743– 1794) designed a calorimeter to measure the metabolic heat...
Fluorescence
Authors: Campbell Iain D.
Published: September 2023

Introduction

Fluorescence occurs when light is emitted from an excited state. A molecular group that fluoresces is called a fluorophore. Naturally occurring fluorophores in biology include tryptophan, the Y-base of t-RNA, NADH, and chlorophyll. A wide range of synthetic fluorescent probes, dyes, and...
Nuclear magnetic resonance
Authors: Campbell Iain D.
Published: September 2023

Introduction

Nuclear magnetic resonance (NMR) is a technique that detects the reorientation of nuclear spins in an applied magnetic field, Bo (Box 6.1). The phenomenon was first demonstrated independently by the Bloch and Purcell groups in 1945. It is extraordinarily versatile...
Oscillators and simple harmonic motion
Authors: Campbell Iain D.
Published: September 2023

The aim of this tutorial is to introduce concepts about simple harmonic motion and driven oscillating systems. These concepts are important for an understanding of a number of topics, including scattering and vibrational spectroscopy.

Oscillating systems are ones that exhibit periodic or cyclic motion....
Electromagnetic radiation
Authors: Campbell Iain D.
Published: September 2023

The aim of this tutorial is to convey the basic properties of electromagnetic radiation: these concepts are essential for understanding Sections 4, 5, 6, and 7 in this book.

Electromagnetic waves

James Clerk Maxwell (1831-1879) combined the laws of electricity and magnetism with those...
Quantum theory and the Schrodinger wave equation
Authors: Campbell Iain D.
Published: September 2023

The aim of this tutorial is to introduce some ideas about quantum mechanics. These are important for understanding spectroscopy (Sections 5 and 6) and aspects of molecular modeling (Section 8).

We can adequately describe the behavior of most objects around us with observable quantities,...
Dipoles, dipole-dipole interactions, and spectral effects
Authors: Campbell Iain D.
Published: September 2023

Dipoles, dipole moments, and their interactions are very important for explaining many properties of molecules that are considered in this book, including non-covalent interactions and spectra. This tutorial sets out some of the key points about dipoles and their interactions.

An electric dipole...
The analytical approach: defining the problem
Authors: Evans E. Hywel , Foulkes Mike E.
Published: September 2023

This chapter explains the six steps to solving a problem in analytical chemistry and defines a problem in a number of scenarios. It outlines a problem solving strategy that is applicable to a range of problems. It also focuses on defining the problem, wherein analysts consider a series of important questions that are analysed in sequence. The chapter explains how analysts evaluate the conditions required to take a suitable sample in order to help answer the main question posed in the first step, such as questions on what should be measured and why should it be measured. It discusses the techniques and methods analysts use in the measurement process.
Sampling
Authors: Evans E. Hywel , Foulkes Mike E.
Published: September 2023

This chapter distinguishes between a homogeneous and a heterogeneous sample and reviews the process for obtaining a representative sample from solids, liquids, and gases. It illustrates a sampling plan to obtain a representative sample and details of a variety of methods used for collecting samples. It also emphasizes the importance of sample preservation and talks about representative sampling, which is a process that considers how to perform the analysis necessary to establish how to take samples safely from the site in a way that is representative of the site itself. The chapter highlights samples that are taken as a representative in a relationship to the property to be measured from the bulk or source material, which is described as being fit for purpose. It elaborates how to obtain a homogeneous sample that is representative of the bulk material.
Sample preparation
Authors: Evans E. Hywel , Foulkes Mike E.
Published: September 2023

This chapter outlines the requirements for sample preparation for solid, liquid, and gaseous samples and details a range of equipment and methodologies used for sample preparation. It examines the development of appropriate sample preparation strategies for samples with varying requirements. It also describes the sample preparation wherein the analyst has to identify the necessary procedures and perform them so that the analyte or property can be readily measured using the chosen method of analysis. The chapter emphasizes how the processes of sample preparation and measurement must be chosen very carefully in order to answer the problem correctly. It discusses how knowing the chemical make-up of the matrix helps formulate how an analyte can be released from the sample itself.
Calibration and quantitation
Authors: Evans E. Hywel , Foulkes Mike E.
Published: September 2023

This chapter details how to prepare a series of working standards to be used for instrument calibration and how to plot a calibration curve and fit a linear trend line. It talks about the of use a calibration curve to calculate the analyte concentration in a sample and distinguishes the different sources of errors that can occur in instrumental analysis. It also explores the actuality of making an analytical measurement and analyses qualitative analysis which is normally referred to as selectivity and considered as a necessary pre-condition. The chapter focuses on qualitative analysis concerned with the identification of an analyte rather than the measurement of its quantity, such as mass spectrometry. This can be used to identify controlled drugs in body fluids for forensic purposes. It illustrates the mass spectrum of morphine, which comprised of fragments of the molecule that have different masses.
Introducing the cell: the unit of life
Authors: Hackney Carole , Furness David
Published: September 2023

This introductory chapter provide an overview of cells, which are the basic unit of life and, with the exception of certain particulate forms that can reproduce under some conditions (viruses), make up all living things. The two main types of cell are prokaryotes, which lack a nucleus, and eukaryotes, which possess a nucleus. Eukaryotes may have evolved from prokaryotes acting together in a communal way initially, until eventually they became associated together within a single membrane. The modern eukaryotic cell is encapsulated in a plasma membrane, which contains a watery cytoplasm within which are a number of organelle types and a nucleus containing the genetic material of the cell. The chapter then looks at membrane systems, cell division, and tissue formation.
Lungs: the cells of the respiratory system
Authors: Shambayati Behdad , Evered Andrew
Published: September 2023

This chapter assesses the tissues and cells involved in respiration. Respiration is the transport of oxygen into cells and tissues, and the removal of carbon dioxide. The respiratory system consists of two parts: a system of tubes and passages for conduction of the air, and a respiratory portion in which gaseous exchange occurs. The conduction portion includes the nose, pharynx, trachea, and bronchi, while the respiratory portion includes respiratory bronchioles, alveolar ducts, and alveoli. Alveoli are sac-like structures that make up the majority of lung tissue and are the sites where exchange of O2 and CO2 takes place. The very thin wall of the alveoli and their close proximity to a dense network of capillaries allows the diffusion of oxygen from inspired air into arterioles, and the removal of carbon dioxide from venules into the alveolar space for removal during expiration.
Fundamental aspects of characterisation methods in inorganic chemistry
Authors: Weller Mark T. , Young Nigel A.
Published: September 2023

This chapter discusses the fundamental aspects of characterization methods in inorganic chemistry. While not all of the techniques described in this book use the electromagnetic spectrum as a probe of the structures of inorganic molecules and materials, four of the main physical methods — NMR spectroscopy, vibrational spectroscopy, X-ray diffraction, and ultraviolet-visible (UV-vis) spectroscopy — all employ light of a specific range of wavelengths. Other less commonly employed techniques, such as Mössbauer spectroscopy, X-ray absorption spectroscopy (XAS), electron paramagnetic resonance (EPR), and nuclear quadrupole resonance (NQR) spectroscopy, also use portions of the electromagnetic spectrum covering the energy range from gamma rays, with wavelengths of a few picometres, to microwaves, with wavelengths of centimetres to metres. Because the full electromagnetic spectrum is employed to characterize inorganic compounds, the data obtained covers a very large wavelength and, therefore, energy range. The chapter then describes energy unit conversions and Fourier transforms in spectroscopy.
Nuclear magnetic resonance (NMR) spectroscopy
Authors: Weller Mark T. , Young Nigel A.
Published: September 2023

This chapter evaluates nuclear magnetic resonance (NMR) spectroscopy. NMR is the most powerful and widely used spectroscopic method for the investigation of the molecular structures of compounds. It yields information about the shape and symmetry of molecules. For many common atom types, NMR spectroscopy defines the different environments present and their numbers. Analysis of NMR spectra often allows the full molecular configuration of a molecule to be determined. The technique also provides useful information about the rate and nature of ligand interchange in fluxional molecules and can be used to follow reactions and so determine their mechanistic pathway. While diffraction techniques usually produce accurate interatomic distances and angles, NMR studies generally yield more limited information on the separation of nuclei, such as which atoms are bonded or close neighbours in a molecule. The chapter then looks at insensitive nucleus enhancement by polarization transfer (INEPT) and COSY (Correlated Spectroscopy) NMR spectrum.
Electronic absorption and emission spectroscopy
Authors: Weller Mark T. , Young Nigel A.
Published: September 2023

This chapter assesses electronic absorption and emission spectroscopy. The electronic absorption and emission spectra of atoms and molecules involve the rearrangement of electrons and provide a wealth of information on the structure and properties of such compounds, as well as their identification. While a variety of electronic transitions are possible in inorganic compounds, the most important are those involving electrons in the d orbitals of transition metal compounds and complexes. Many of these transitions have energies in the visible region of the electromagnetic spectrum, or just outside it in the ultraviolet (UV) or near infrared (NIR). As most of the electronic transitions are in the UV and visible regions of the electromagnetic spectrum, electronic spectroscopy is also often known as UV-visible spectroscopy, shortened to UV-vis spectroscopy. If the spectral range is extended to include the NIR, then it is known as UV-vis-NIR spectroscopy.
Translation of messenger RNA
Authors: Elliott David , Ladomery Michael
Published: September 2023

This chapter covers the process of mRNA translation. Itbegins by reviewing the structure and function of the essential machinery of translation, namely the ribosome and transfer RNA. The chapter outlines the three phases of translation: initiation, elongation, and termination. It also discusses several ways in which mRNA translation can be regulated. The chapter details how ribosomes catalyse the synthesis of polypeptide chains that form when amino acids are covalently linked through peptide bonds. The chapter explains that ribosomes are made up of large and small subunits that contain ribosomal RNA (rRNA) and a multitude of ribosomal proteins. The chapter then looks at the different components of the ribosomal subunits that are distinguished according to the rate at which they sediment, as measured in Svedberg units.
Biochemical investigations and quality control
Authors: Cameron David
Published: September 2023

This chapter discusses the roles of the clinical biochemistry laboratory in the diagnosis, treatment, monitoring, and prognosis of disease states. The equipment used to analyse clinical samples is often complex and large laboratories will produce many thousands of results daily. However, advances made in automation, robotics, and computing have made it possible to cope with ever-increasing workloads, even when the numbers of staff are reduced. Specialist tests are often performed on clinical samples at regional centres where the required expertise is available and to reduce duplication of expensive equipment. In contrast, point-of-care testing (POCT) is increasing and although presenting numerous benefits, it presents a new challenge to the clinical laboratory. Quality control is essential for all assays and when utilized properly gives confidence to the laboratory staff and to users of the service with regard to precision and accuracy of all the tests performed.
Reproductive endocrinology
Authors: Laing Ian , Thornton Julie
Published: September 2023

This chapter studies reproductive endocrinology. Reproductive function in both sexes is a controlled process involving hormones of the hypothalamus, pituitary, and the gonads. The main functions of the ovary are to produce a single egg (oocyte) for ovulation each month and to secrete oestradiol and progesterone, which regulate the uterine cervix and the endometrium to permit the passage of motile sperm and to provide a suitable environment for implantation of a fertilized oocyte. Ovarian function ceases abruptly at the menopause with the exhaustion of the ovarian follicle pool when most women still have a considerable life expectancy. Meanwhile, spermatogenesis is a continuous process in the male and the cyclical changes in gonadotropin production are not evident. The chapter then considers the disorders of reproductive function, including polycystic ovary syndrome. By making use of exogenous steroid hormones it is possible to regulate the function of both the ovaries and the testis.
Therapeutic drug monitoring
Authors: Whelpton Robin , Brown Nigel , Flanagan Robert
Published: September 2023

This chapter studies therapeutic drug monitoring (TDM), which is the term used to describe the measurement of the plasma concentrations of a drug and/or any pharmacologically active metabolite(s) attained during treatment. The aim of TDM is to help optimize treatment by, for example, selecting a dose that maximizes the desired effect(s) of a drug, while minimizing the risk of toxicity. For most drugs, there is a wide margin (so-called margin of safety) between the clinically effective dose and the dose associated with marked adverse effects. However, for some drugs the difference between a clinically effective dose and a potentially toxic dose is small. These drugs are said to have a small ‘therapeutic range’ or narrow ‘therapeutic window’, and the dose of the drug must be adjusted carefully for each patient. In order to appreciate the reasons for TDM and the decisions that may have to be made in dose adjustment, it is necessary to understand what is meant by a ‘drug’, how drugs are given, what the body does to a drug, and how the effect of dose adjustment on the plasma concentration of a drug may be predicted.
Addition Reactions of Alkenes and Alkynes
Authors: Okuyama Tadashi , Maskill Howard
Published: September 2023

This chapter begins with a discussion on the functional groups of alkenes and alkynes: carbon-carbon double and triple bonds. It highlights that the simplest alkene is ethene (ethylene) which acts as a plant hormone controlling the maturation of flowers and fruit. The chapter then reviews the regioselectivity and stereochemistry of electrophilic addition to alkenes. It argues that the characteristic reactions of alkenes and alkynes are addition reactions which may be initiated in various ways depending on the nature of the alkene (or alkyne) and the reagent. The chapter then presents the most common reaction of simple alkenes: electrophilic addition. It also looks at the electrophilic attack at 1,3-dienes which leads to both 1,2- and 1,4-addition products. Finally, it concludes by explaining the Diels-Alder reactions and the epoxidation of alkenes. It also considers the cyclopropanation of alkenes with carbenes and carbenoids and the hydrogenation of alkenes and alkynes.
Molecular Structure and Shapes of Organic Molecules
Authors: Okuyama Tadashi , Maskill Howard
Published: September 2023

This chapter examines the shapes of organic molecules. It investigates what molecules look like and why molecules have a particular shape. The chapter reveals that three-dimensional shapes of simple molecules are the result of electrostatic repulsion between electron pairs and can be explained in terms of shapes of molecular orbitals involved in chemical bonding. The s and p atomic orbitals may be transformed into hybrid atomic orbitals with different shapes which lead to two types of covalent bonds, σ and π, and account for the various shapes of molecules. Next, the chapter elaborates on the meaning of isomers. Isomers are different compounds with the same molecular formulas. The chapter then displays the two principal kinds of isomers: constitutional isomers and stereoisomers.
Stereochemistry and Molecular Chirality
Authors: Okusecyama Tadashi , Maskill Howard
Published: September 2023

This chapter discusses three-dimensional structures of molecules and their mirror images. It then presents further types of stereoisomerism which occur when a molecule and its mirror image are not identical. The chapter notes that some molecules have the property of handedness or chirality, which relates to the non-superposability of mirror image forms. Most naturally occurring organic compounds have this property and the biochemical world, in general, is chiral at the molecular level; consequently, chirality is tremendously important in the chemistry of life. The chapter displays how chirality occurs in molecules, and introduces some of its consequences in chemical reactions. It concludes by elaborating on enantiomers and diastereoisomers, optical activity, and prochirality.
Reactions of Nucleophiles with Alkenes and Aromatic Compounds
Authors: Okuyama Tadashi , Maskill Howard
Published: September 2023

This chapter explores the reactions of nucleophiles with ?, ?-unsaturated carbonyl compounds and related electrophilic alkenes as well as with aromatic compounds carrying a nucleofuge - usually haloarenes. It looks at the kinetic and thermodynamic control of carbonyl and conjugate additions, then reviews the nucleophilic addition to other electrophilic alkenes. The chapter then investigates the substitution reactions of highly electrophilic arenediazonium ions (which have an excellent nucleofuge, N2) by the SN1 and other mechanisms. It then looks at Michael reactions (or Michael addition) and Robinson annulation. Finally, the chapter considers nucleophilic aromatic substitution by addition-elimination and elimination-addition mechanisms.
Chromosomes and Cellular Reproduction
Authors: Thomas Alison
Published: September 2023

This chapter discusses chromosomes and cellular reproduction. Living organisms are classified as prokaryotes or eukaryotes. Eukaryotic cells have a more complex structure, and each eukaryotic species has a characteristic number of chromosomes. Each eukaryotic chromosome contains a single long linear deoxyribonucleic acid (DNA) molecule which is tightly packed. The chapter looks at sex chromosomes and sex determination, before considering the cell cycle. The cell cycle describes the different stages that a eukaryotic cell passes through from one cell division to the next. The chapter then explains mitosis and meiosis. Mitosis results in the production of two genetically identical cells and meiosis leads to the formation of four genetically variable cells with half the chromosome number.
Chromosome Mutations
Authors: Thomas Alison
Published: September 2023

This chapter discusses chromosome mutations, during which one or a few chromosomes may be lost or gained (aneuploidy). Common aneuploid conditions include monosomy and trisomy; nullisomy and tetrasomy also occur. The addition of whole sets of chromosomes produces polyploid cells. Meanwhile, segments of individual chromosomes can be deleted, duplicated, become incorporated in other chromosomes, or inverted. Chromosome mutations often arise through errors during meiosis. In turn, chromosomal mutations frequently disrupt the process of meiosis, resulting in unbalanced gametes. The chapter then looks at how changes in chromosomal structure and number often occur in tumour cells. It also considers how chromosome mutations play important roles in evolution.
Genetics of Populations
Authors: Thomas Alison
Published: September 2023

This chapter examines population genetics, which analyses the patterns of genetic variation shown by groups of individuals, i.e. by populations. This contrasts with the main concern of Mendelian genetics and, to a large extent, of quantitative genetics, as both focus on the genotype of individuals and the genotypes resulting from single mating. Population genetics explores the evolutionary processes that shape a population’s genetic variation, i.e. mating systems, migration, mutation, population size, and selective forces. The chapter then considers how the analysis of genetic diversity in populations of endangered species helps formulate conservation policies. Ultimately, the genetic variation within and between different populations is described in terms of frequencies of alleles and resulting genotypes. The chapter looks at the Hardy–Weinberg equilibrium, non-random mating, natural selection, and genetic drift.
Working with Genes: Analysing and Manipulating DNA
Authors: Thomas Alison
Published: September 2023

This chapter explores the process of analysing and manipulating deoxyribonucleic acid (DNA). A wide range of molecular biology techniques enables DNA to be manipulated and analysed, yielding information about the nature and function of genes. The terms recombinant DNA technology, DNA cloning, and gene cloning all refer to the same process, namely the transfer of a DNA fragment from one organism to a self-replicating genetic element that replicates the fragment in a foreign host cell. Multiple copies of a DNA sequence can be produced by cloning or by using the polymerase chain reaction. Genes are isolated from DNA libraries and gel electrophoresis separates different-sized DNA fragments. Meanwhile, the nucleotide sequence of a segment of DNA is determined by Frederick Sanger’s dideoxy method or next generation sequencing methods. Finally, forward and reverse genetics are different analytical approaches to linking phenotype and genotype.
Microbodies
Authors: Wang Qiuyu , Smith Chris , Davis Emma
Published: September 2023

This chapter identifies microbodies as globular-shaped organelles surrounded by a single biological membrane. It highlights three types of microbodies that are recognizable in different types of cells: peroxisomes, glyoxysomes, and glycosomes. It also describes peroxisomes as roughly spherical organelles that are widely distributed in eukaryotes and enriched in urate and d-amino acid oxidases and catalase activities. The chapter examines glyoxysomes, which are specialized peroxisomes found particularly in plant lipid storage structures, such as the endosperm or the cotyledons of germinating seeds and occur in filamentous fungi. It considers glycosomes as membrane-enclosed organelles which occur in a relatively few species of protozoa called trypanosomes.