bluuebunny/crossref_metadata_2025 huggingface dataset:
The properties of solids
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter describes the electrical, optical, and magnetic properties of solids, tracing the origins of phenomena that are the basis of the design of a variety of useful devices, such as lasers, light-emitting diodes, and powerful magnets. It points out how modern technology depends on an understanding of the physical properties of solids. It also outlines the electrical, optical, and magnetic properties of solids that stem from the properties of their constituent atoms and their interactions. The chapter explores electronic conductors that are classified as metallic conductors or semiconductors according to the temperature dependence of their conductivities. It talks about an insulator, which is a semiconductor with a very low electrical conductivity.
Colligative properties
Authors: Atkins Peter , Paula Julio de , Smith David
Published: September 2023

This chapter evaluates colligative properties. A colligative property is a property that depends on the number of solute particles, not their chemical identity; they arise from the effect of a solute on the entropy of the solution. Colligative properties include lowering of vapour pressure, depression of freezing point, elevation of boiling point, and osmosis. The phenomenon of osmosis is the passage of a pure solvent into a solution separated from it by a ‘semipermeable’ membrane, a membrane that is permeable to the solvent but not to the solute. The osmotic pressure is the pressure that must be applied to the solution to stop the inward flow of solvent. The chapter then considers how the van 't Hoff equation expresses the osmotic pressure in terms of the concentration of solute in the solution.
Energy, temperature, and chemistry
Authors: Atkins Peter , de Paula Julio , Smith David
Published: September 2023

The concept of energy occurs throughout chemistry. Some reactions release energy; others absorb it. Bond formation is accompanied by a lowering of energy; bond breaking requires energy. Almost every structure and almost every reaction can be discussed in terms of energy, and the precise meaning...
Fundamentals
Authors: Elliott Joanne , Page Elizabeth
Published: September 2023

This chapter focuses on the units which are fundamental to the understanding and application of physical chemistry. It describes the Système International d'Unités (SI) system of units. This has been in use since 1970 and consists of seven base units, of which six are commonly used in chemistry. These measure mass, length, time, electrical current, temperature, and amount of substance. There is a seventh unit, namely luminous intensity, but this is only rarely relevant in chemistry. The chapter includes activities that determine the derived units for kinetic energy. These activities show that the unit for potential energy is equivalent to that of kinetic energy.
Phase equilibrium
Authors: Elliott Joanne , Page Elizabeth
Published: September 2023

This chapter discusses phase, which is a form of gas, liquid, solid, or supercritical fluid which is uniform in its chemical composition and its physical state. The chapter emphasizes that 'vapour' is used to describe the gaseous phase of substances which are liquids or solids at room temperature. The chapter also looks at 'vapour pressure', which is the equilibrium partial pressure exerted by a liquid in a sealed container at a fixed temperature. The chapter also covers the phase behaviour and phase transitions of one-component systems. The chapter includes a mention of the phase behaviour of two-component mixtures, such as the phenomena of colligative properties. It explores the term 'ideal gas', which refers to a system where the gaseous molecules experience no intermolecular forces.
Electrochemistry
Authors: Elliott Joanne , Page Elizabeth
Published: September 2023

This chapter describes an electrolyte, which is a substance that dissociates into its component ions upon dissolution and produces a solution that conducts electricity. It examines the variable conductivity of electrolytes, in which small ions tend to be more conductive than large ions. It also points out that the total number of ions in a solution determines overall conductivity. The chapter discusses the ion–ion interactions that influence the behaviour of the electrolyte and the position of species in the electrochemical series, which determines the reactivity of the solution. It cites electrochemical processes which involve an exchange of electrons, noting that oxidation is the loss of electrons and reduction is the gain of electrons.
Isomerism
Authors: Cook Michael , Cranwell Philippa
Published: September 2023

This chapter discusses isomerism, which describes the different ways in which we can arrange the atoms in a molecule with a fixed formula. This arrangement of atoms can take the form of constitutional (structural) isomerism, where the atoms are joined in a different order, or stereoisomerism, where the atoms are arranged differently in space. Stereoisomerism is subdivided into conformational isomerism and configurational isomerism. Two conformational isomers can be converted into each other (interconverted) by rotation around single bonds, whereas configurational isomers cannot be interconverted without breaking a bond. The chapter also discusses cis/trans isomerism and optical isomerism (chirality). Cis/trans isomers arise when rotation is restricted at a particular point in a molecule, most commonly due to a carbon–carbon double bond. This restricted rotation allows groups positioned on either side of the double bond to either sit adjacent to each other (cis), or opposite each other (trans).
Introduction
Authors: Bromham Lindell
Published: September 2023

This introductory chapter provides an overview of the kind of information that can be gained from analysing DNA sequences. The analysis of DNA sequences contributes to evolutionary biology at all levels, from dating the origin of the biological kingdoms to untangling family relationships. The chapter illustrates the information that can be gained from the analysis of DNA sequences by considering a single DNA sample and how it can shed light on the evolutionary history of individuals, families, social groups, populations, species, lineages, and kingdoms. The aim of this book is not to provide protocols for DNA sequencing or instructions for software packages used in the production and analysis of DNA sequences. Instead, it presents the background knowledge one needs to understand these techniques.
Replication
Authors: Bromham Lindell
Published: September 2023

This chapter examines DNA replication. The evolution of life depends on hereditary information being copied from one generation to the next. Thus, a basic grasp of DNA replication is essential for anyone wishing to understand evolution. Moreover, familiarity with the processes of DNA replication is the key to understanding many molecular techniques. DNA amplification (making millions of copies of a DNA sequence in the laboratory) relies upon the domestication of the DNA copying processes that occur in living cells. Understanding DNA replication is also central to appreciating the nature of biological information stored in DNA. DNA replication creates a nested hierarchy of differences between genomes that reveals the relationships between organisms and the processes of evolution.
Genome
Authors: Bromham Lindell
Published: September 2023

This chapter evaluates genomes. Genome size varies dramatically between species. Much of the variation is due to repeated sequences, rather than differences in number of different genes. Whole genome duplications can provide the raw material for establishing new lineages. On a finer scale, shorter repeat sequences are prone to accidents in replication that increase or decrease the number of copies. Because of this high rate of change, short repeats are likely to vary in number between individuals. Other repeat sequences play a more active role in their own duplication, containing regulatory signals and genes that cause them to be copied and inserted throughout the genome. Transposable elements not only fill the genome with copies of themselves, they also remodel their host's genome. The changes caused by these 'jumping genes' have profound effects on genome structure and evolution.
Gene
Authors: Bromham Lindell
Published: September 2023

This chapter focuses on genes, which, on their own, are inert. It is only when they are transcribed (copied into RNA) that they can influence an organism's development, morphology, and behaviour. The expression of genes requires the co-ordinated interaction of a great many sequences, not only the gene itself but the regulatory sequences that control its expression and the genes that make the biochemical equipment needed for transcription and translation. Typically, for molecular phylogenetics, we are interested in the genotype (the information in the genome) rather than the phenotype (the form and function of the individual that develops from that genome). However, it is important to understand the role of a sequence in the formation of phenotype in order to appreciate the different patterns of evolution we see in different parts of the genome.
Dates
Authors: Bromham Lindell
Published: September 2023

This chapter examines how DNA can provide temporal information: the longer genomes evolve separately the more different they will be. For molecular dates, we should expect the confidence intervals to be quite wide, because there are so many things that can influence the number of substitutions that accumulate in a lineage over time. Given that we rarely know what the underlying rates are, our confidence limits must include our uncertainty in the patterns of rate evolution, as well as the possible effect on date estimates of the various assumptions inherent in our models. Sometimes our confidence intervals might be formally expressed as a distribution of values derived from statistical analysis, other times they may represent the upper and lower estimates obtained by varying the assumptions on which the date estimates are based. The fossil record remains the primary source of information on the evolutionary past.
Introduction
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter gives an overview of neuroethology, the biological discipline that attempts to understand how the nervous system controls the natural behavior of animals. It emphasizes that this area of study has its roots in both neurobiology and ethology, and that its success is based on the incorporation of a blend of the neurobiological and ethological approaches into its own scientific armory. The chapter introduces ethogram, which refers to the entire behavioral repertoire of an animal species. Then it discusses how behavioral patterns are quantified using their rate of occurrence, duration, and/or intensity. The chapter also considers how to select a suitable model system for neuroethological research. These systems are characterized by behavioral patterns that, although simple, robust, and readily accessible, are also ethologically relevant.
Sensorimotor integration
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter focuses on sensorimotor integration or the transformation of the processed sensory input into proper motor action. It particularly looks at the jamming avoidance response of the weakly electric fish Eigenmannia as a model system that provides an excellent example to illustrate how sensory information and motor programs are integrated to generate a biologically important behavior pattern in response to a stimulus. Fish of this genus continuously generate, by means of an electric organ, wave-type electric discharges. The discharge rate is determined by the frequency of the pacemaker nucleus, an endogenous oscillator in the medulla oblongata. The fish sense their own electric currents, as well as those of neighbors, through electroreceptors. The chapter also discusses the electrosensory lateral line lobe, torus semicircularis, and nucleus electrosensorius.
Communication
Authors: Zupanc Günther K. H.
Published: September 2023

This chapter reviews the biological definition of communication and some of the sensory modalities involved in the detection of communication signals. It explains the concepts of true communication and mutualism, as well as the sensory modalities involved in communication. The discussion covers visual, acoustic, chemical, tactile, and electrical signals. Furthermore, the chapter focuses on two intensively studied model systems. One of the model systems is the neuroethology of cricket song where the mechanism and neural control of sound production are examined, and the concept of positive phonotaxis is explained. The discussion covers the use of Kramer locomotion compensator, the song recognition by auditory interneurons, as well as the effect of temperature on calling songs of crickets. The second model system explains the development of bird songs — describing the neural circuits for song perception, song production, and song learning.
Receptors and Signal Transduction
Authors: Rostron Chris
Published: September 2023

This chapter discusses receptors and signal transduction. Receptors are proteins or glycoproteins, which are very important targets for drug action. They are part of the communication systems within the body. The interaction of the appropriate endogenous ligand with a receptor results in a specific biochemical or physiological response. This response is referred to as signal transduction. Drugs which bind to such receptors can activate or inhibit the normal response associated with that receptor. The chapter begins by explaining cellular communication. Then, it looks at the nature of ligand-receptor interactions. It also considers the four main types of receptors: ion channel receptors, G-protein-coupled receptors, tyrosine kinase receptors, and nuclear receptors.
Nucleic Acids and Protein Synthesis as Drug Targets
Authors: Rostron Chris
Published: September 2023

This chapter evaluates nucleic acids and protein synthesis as drug targets. The nucleic acids, DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are responsible for the storage and processing of the genetic information of all types of cells. Sequences of DNA carry instructions for protein synthesis, with one of the roles of RNA being an intermediate in this process. Many drugs, such as antibacterial, antiviral, and anti-cancer drugs, target nucleic acids and protein synthesis. Some classes of anti-cancer drugs bring about their activity by interfering with the normal structure of nucleic acids. Other classes of anti-cancer drugs target the synthesis of nucleic acids. They do so at all stages of nucleic acid synthesis, namely transcription, translation, and replication. The chapter also considers viruses as drug targets before looking at antisense drugs.
Pharmacogenetics and Pharmacogenomics
Authors: Rostron Chris
Published: September 2023

This chapter traces the development of the science of pharmacogenetics and the clinical importance of polymorphisms of certain metabolic enzymes. It also examines the potential and challenges that the relatively new science of pharmacogenomics presents for the process of drug design. The science of pharmacogenetics has a long history dating back to the 1930s but was initially linked to empirical observations regarding, mainly, drug metabolism. The chapter distinguishes between cytochrome P450 2D6 (CYP2D6) polymorphism and cytochrome P450 2C9 (CYP2C9) polymorphism. It looks at methyltransferase polymorphism and idiosyncratic adverse drug reactions. Finally, the chapter considers phase II pharmacogenetics, before studying the clinical relevance of pharmacogenetics and pharmacogenomics.
Tropospheric chemistry—precipitation
Authors: VanLoon Gary W. , Duffy Stephen J.
Published: September 2023

This chapter looks at the activities and chemical processes that influence the chemistry of precipitation, particularly the issues surrounding nitrogen and sulfur atmospheric chemistry and the methods used to control their emissions. It discusses the composition of natural precipitation and how the chemistry of various forms—rain, snow, and fog—is affected by both natural and anthropogenic influences. It also examines the atmospheric production and removal of nitric and sulfuric acids, the two most prominent anthropogenic emissions influencing the pH of precipitation. The chapter highlights the global situation and the sources and sinks of nitrogen and sulfur compounds, using aggregate fluxes and their influence on the chemistry of precipitation around the globe. It features some of the technology and related chemistry for controlling emissions of nitrogen and sulfur oxides.
Quantum Chemistry
Authors: Harvey Jeremy
Published: September 2023

This chapter discusses quantum chemistry. Pretty much all of computational chemistry relies on quantum mechanics in the sense that molecular systems follow the laws of quantum mechanics. But ‘quantum chemistry‘ has a more specific meaning: it is the study of chemistry through the use of approximate solutions to the electronic Schrödinger equation. The chapter describes the background and principles of quantum chemistry, with a focus on the conceptually most important approximate approach, which is Hartree–Fock theory. In principle, the time-dependent Schrödinger equation could be used to predict what happens in chemical reactions. The basic approximation in Hartree–Fock theory is an assumption that electrons move independently of one another throughout the molecular system. The chapter then looks at the calculation of a Hartree–Fock wavefunction.
Dynamics Methods
Authors: Harvey Jeremy
Published: September 2023

This chapter focuses on dynamics methods. Especially for complex systems, the ‘static’ inspection of features of the potential energy surface is not sufficient to predict the behaviour of the system described by it. Simulation techniques sample the range of structures that are visited under particular experimental conditions. Molecular dynamics simulations perform this sampling by applying Newton’s laws of motion to the atoms. On the other hand, Monte Carlo simulations use random changes of structure, with an algorithm for accepting or rejecting given changes that results in an overall Boltzmann distribution. Sampled structures can be analysed in terms of average properties, for example using radial distribution functions. The most common application of dynamical simulation methods is the study of biomolecules, their structural variability, and their interactions with other molecules.
Bonding and Molecular Shape
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter discusses bonding and molecular shape of electrons. A covalent bond occurs when atoms share a pair of similar electrons. Modern theories on covalent bonding are dominated by molecular orbital theory. Polar covalent bonds occur when different atoms share the electron pair unequally due to electronegativity. With benzene being the most familiar molecule of the bonding, delocalization happens when more than two atoms are involved in the bonding. The valence-shell electron-pair repulsion (VSEPR) theory can help us to visualize the shapes of simple molecules. Additionally, ionic bonding occurs when an atom transfers an electron to another atom and the ions formed a crystal lattice electrostatically.
Acid–base Equilibrium
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter explains the acid-base equilibrium. This involves the transfer of protons in line with the Brønsted–Lowry theory. A strong acid or strong base is fully ionized in an aqueous solution, while weak acids or bases are only partially ionized in an aqueous solution. Acid-base titrations measure the unknown concentration of one solution by reaction with another standard solution with a familiar concentration. The chapter also notes how indicators are typically water-soluble weak organic acids with varying colours at different pH values. It explores the alternative theory of acid-base reactions proposed by Gilbert Lewis: a Lewis acid is an electron-pair acceptor, while a Lewis base is an electron-pair donor.
The Halogens
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter discusses the halogens, also known as either Group 17 or Group VII. It also notes the exception of featuring astatine due to its high radioactivity. The physical properties of the halogens range between the melting points, boiling points, atomic radius, ionic radius, electronegativity, ionization energy, and dispersion forces. Additionally, the oxidizing ability of the halogens decreases in positivity, while the reducing ability of the halide ions increases. Fluorine is known to be exceptionally strongly oxidizing. Aqueous halide ions are tested by adding aqueous silver nitrate acidified with dilute nitric acid. An equilibrium is set up when chlorine dissolves in water.
Transition Metals 1
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter discusses the halogens, also known as either Group 17 or Group VII. It also notes the exception of featuring astatine due to its high radioactivity. The physical properties of the halogens range between the melting points, boiling points, atomic radius, ionic radius, electronegativity, ionization energy, and dispersion forces. Additionally, the oxidizing ability of the halogens decreases in positivity, while the reducing ability of the halide ions increases. Fluorine is known to be exceptionally strongly oxidizing. Aqueous halide ions are tested by adding aqueous silver nitrate acidified with dilute nitric acid. An equilibrium is set up when chlorine dissolves in water.
Transition Metals 2
Authors: Clugston Michael , Stewart Malcolm , Birembaut Fabrice
Published: September 2023

This chapter focuses on the first row of transition metals ranging from tin to copper. It clarifies how scandium and zinc are not transition metals due to their oxidation states and d subshells. The group has d-block elements with at least one stable ion that has a partially-filled d subshell. Transition metals showcase variable oxidation states. An acidic solution with a reductant can reduce a transition metal ion, while an alkaline solution with an oxidant could oxidize a transition metal. The stability of the high oxidation states can be significantly increased in alkaline solutions. The chapter also notes how transition metals are often used as catalysts.
Sum over states: the molecular partition function
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

This chapter explains the molecular partition function in the context of applying the Boltzmann law. It discusses the equations for molecular energy states alongside diagrams for clarification. Next, the chapter previews the importance of the molecular partition function under the thermodynamic calculations in a macroscopic assembly of particles. It notes the molecular partition function q, which determines the particle distribution over accessible quantum states. In addition, the chapter characterizes the closeness of spacing in the energy manifold by referring to the density of state functions. It adds how partition functions can be modified by taking into account that quantum states can be degenerate, with a number (g) of states all sharing the same energy.
The ideal diatomic gas: the vibrational partition function
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

This chapter discusses the ideal diatomic gas in terms of the vibrational partition function. It explains that the value of the vibrational partition function at 300K is imperceptibly different from unity. It states that this approximation can be applied to light molecules. The chapter uses the diatomic SHO model as a reference to classical vibrational frequency. It highlights that vibrational energy levels in diatomic molecules are always non-degenerate. This should be taken into consideration when handling polyatomic species. Additionally, the chapter discusses high-temperature limiting behaviour, the canonical partition function, zero-point energy, heat capacity, and entropy in relation to the vibrational partition function. It also lists other immediate forms of rotational or vibrational motion, such as torsional oscillation, internal rotation, and free rotation.
Calculating equilibrium constants
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

This chapter explains the calculation of equilibrium constants. Deriving the relationship between partition functions and equilibrium constants provides a greater understanding of the true nature of chemical equilibrium. The chapter discusses molar Gibbs free energy to calculate perfect gases. It also looks at the equation, aspects, interpretation, and calculations for equilibrium constants. The chapter also tackles calculation problems of five different equilibria, including dissociation, isotopic exchange, and the water-gas shift reaction. Finally, the chapter highlights that statistical thermodynamics is not bounded by the limitations discussed in the book, which aims to foster understanding of key concepts through the discussion of ideal examples and does not consider the highly complex cases one would encounter in the real world.
The Emergence of Life on Earth
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter explains how life emerged and looks at the subsequent development of understanding life. All modern living organisms are cellular, and looking at the characteristics of cells provides some ideas about the locations where and when life may have originated, and when this might have occurred. Geochemistry shows how some of Earth's dominant global features are the result of its formation history and accretionary environment. The chapter discusses the notion that life is based on aqueous organic chemistry. The chemistry of carbon is a known example of functioning biology. It also covers the correlation between DNA, RNA and functional proteins.
Size and Scale
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter looks into size and scale in correlation to scientific notation and standard form. It explains that order of magnitude is used to mean a rough measure of the size of something expressed as a power of 10 and it is also used in a relative sense. Instead of adding into the equation, the use of a logarithmic scale is more convenient when trying to fit measurements onto a linear scale. The chapter then considers the difference between logs to the base 10 and natural logarithms (ln) and logs to the base e. The chapter then examines the magnitude of numbers and scientific notation and the conversion of numbers from scientific notation to prefixes.
Ratio and Proportion
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter focuses on the expression and comparison of ratio and proportion. The ideas of ratio and proportion can be expressed using a variety of symbols. Their notation is often used interchangeably when describing these ideas. A part-to-whole ratio is often expressed as a fraction, especially since a diagram can be a helpful way to visualise ratio. The chapter also considers the notions of probability and the term concentration in relation to the notion that solutions can be expressed as the mass of a substance per volume. It then considers the dilution of a solution which is carried out to make the concentration ten times less.
Understanding Samples
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter looks at samples and statistics by referencing populations and parameters. It explains how the population encapsulates all the possible observations people could make when attempting to answer a particular question, while the parameter uses all the data in the population to calculate a descriptive statistic. In bias and random sampling, some thought should be put into the selection of objects to measure and contain data, as the sample should truly be representative of the population. The chapter also notes the importance of sample size and sample quality as key determinants of statistical power. It explores how related and unrelated samples are calculated to understand the independence of data.
Building Blocks
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter discusses the building blocks of molecules and macromolecules. It cites the importance of understanding chemical compounds and chemical reactions in biology. Key properties of molecules, including their size, shape and reactions, are determined by the atoms that make them up and the ways these are bonded together into functional groups. The chapter examines the structure and function of biological macromolecules, referencing the four main classes: carbohydrates, lipids, nucleic acids, and proteins. It also discusses the function and structure of water, which holds a key role in supporting life.
Energy
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter considers the notion of energy. Energy underpins the maintenance of life. Living cells resemble chemical factories within which thousands of reactions take place, and each reaction involves transformations of matter and energy. The chapter explains the function and features of adenosine triphosphate (ATP) as a universal energy currency. It also outlines the principles of food oxidation and the harnessing of energy. Enzymes act as biological catalysts because they lower the activation energy required before a reaction can happen. The chapter also tackles the electron affinity of electron carriers or hydrogen carriers. These determine what can donate electrons.
Information
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter looks at genes and genomes, and references the chemical structures of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). It notes the two-stage process of protein synthesis, which are transcription and translation. DNA replication is extremely accurate. However, damaged DNA can be repaired by the use of direct repair and excision repair mechanisms. However, it should be noted that the repairs are error-prone and may lead to cancer. The chapter mentions that DNA replication is semi-conservative, so each strand acts as a template for the polymerization of complementary nucleotides. The chapter also looks into genome organization and packaging in prokaryotic and eukaryotic cells.
Reading the Genome
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter provides an overview of gene expression and protein synthesis, which have two main phases: transcription and translation. It explains how cells utilize the information stored in their genome. Most genes encode proteins are synthesized via the expression of an intermediate RNA molecule called a messenger RNA (mRNA). However, some genes encode other types of RNA not destined to be translated into protein. Thus, gene expression is regulated mainly at the level of transcription, by DNA-binding proteins that bind regulatory sequences in gene promoters. The chapter details the process of RNA synthesis through transcription and protein synthesis through translation.
Metabolism
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter covers the release of energy from glucose, fats, and amino acids during the process of metabolism. It explains that biological oxidation involves the removal of electrons and their transfer to another acceptor molecule and the enzymatic removal of two hydrogen atoms from a metabolite molecule. The main stages of glucose oxidation include the outline of the pathway of glycolysis in terms of ATP production and reduced coenzymes. The chapter then looks into anaerobic respiration and fermentation, which involves the production of ATP without the use of oxygen. It also explains the synthesis of metabolic fuels by plants through the process of photosynthesis.
Viruses
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter focuses on the structure and features of viruses. It explains that viruses are entirely parasitic and dependent on a host cell for replication. Viruses have a significant effect on many ecosystems due to their influence on nutrient availability, species diversity, and even climate change via the release of carbon from dead hosts. Viruses can cause significant suffering and death on a global scale and economic scale. The chapter examines the diversity of viral replication strategies, such as replication in DNA and RNA viruses. It considers phage therapy, pest control, and molecular research as the other uses of viruses.
Cardiovascular System
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter details the function and features of the cardiovascular system. The cardiovascular system acts to deliver nutrients to cells and remove waste products prior to excretion, while also playing a vital role in communication between cells and organ systems by transporting important signalling molecules. The cardiovascular system consists of the heart, vascular system, and blood and these collaborate to maintain homeostasis. The chapter explores the composition and function of blood, which moves around the body by virtue of the contraction of the heart. It also mentions that blood is a mixture of different cell types suspended in a fluid matrix.
The Structure of Living Organisms
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter focuses on the structure of living organisms. The basic units of life, particularly when it comes to cells and the organelles inside them, are enclosed structures bounded by membranes. Biochemistry helps in unveiling and investigating the structure and function of cells, which are identified to be self-contained units of life. The chapter then details differentiation as the process of cell specialization. This happens even though all cells in an organism have similar genetic composition. It explores the link between the tissues of multicellular animals and multicellular plants while explaining that both require mechanisms for the internal coordination of cellular activity based on chemical signals and electrochemical transmissions conducted by nerve tissues.
Interaction with the External Environment
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter considers the environmental variables that influence the survival and reproduction of organisms. Living organisms, their structures, and their life processes evolved from ancestral organisms through a combination of variation and selection. The forces of selection act on the phenotype of individuals, so genes are not particularly under selection pressure directly. The chapter explains how light, geography, gravity, and the electromagnetic spectrum affect most biological processes. It then argues that plants and animals must adapt to the imperatives of the gaseous environment and the physical imperatives of heat transfer to and from the environment to survive and reproduce.
Genes
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter explores evolutionary change in alleles, genotypes, and phenotypes. It covers variation between populations by looking at the relative abundance of organisms with phenotypes, genotypes, or alleles. Unlike natural selection acting on genotype, evolution refers to a change in the genetic makeup of a population over time resulting from specific selection pressures. The chapter enumerates the main processes responsible for a population's genetic change: mutation, natural selection, genetic drift, non-random mating, and gene flow. It then examines the Hardy-Weinberg equation, which enables the correlation between genotype frequencies and allele frequencies in a stable population in an effort to test whether evolution is occurring in a given population.
Solutions
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter looks into solutions to the threats to ecosystems. Solutions addressing the threats can be largely grouped under the following: protection, management, conservation, and restoration of ecosystems. The chapter explains how conservation can either occur in capacity or the wild. It clarifies that ecological management is not only about conservation as it involves managing ecological problems, such as a pest or disease damaging other species or human livelihoods. The key aspects of restoration ecology include recreating habitats, rewilding landscapes, and reintroducing species. The chapter also acknowledges the importance of other landscape-scale conservation approaches, such as working with farmers.
Evolutionary Processes
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter looks at the concept of evolutionary processes. It explains that life on Earth is the culmination of evolutionary processes which have been occurring across the millennia since life first emerged. According to Darwin's evolutionary theory, life changes over time, and these changes are passed down through the generations. Some processes can trigger evolutionary change, such as natural selection, migration, mutation, non-random mating, and genetic drift. The chapter then considers the importance of studying evolution for the understanding of biological sciences. It also discusses the development of the theory of natural selection.
The Diversity, Organization, and Classification of Life
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter discusses the diversity, organisation, and classification of life. It talks about the natural human tendency of grouping and identifying things with appropriate labels. Taxonomy is the term used for the naming and grouping of biological organisms. The resulting collection of names forms a biological nomenclature. The chapter discusses the traditional, Linnaean taxonomic approach that categorizes all living organisms into the broad categories of Plantae or Animalia and the systematic interpretation of organismal relationships. It then looks into the pitfalls of taxonomic interpretations, for example, fixed classification and misleading names.
Molecular Tools and Techniques
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter explores the usage of molecular tools and techniques. It acknowledges the rapid expansion and increasing power of DNA technology and genetic engineering. Since cellular DNA molecules are extremely large, basic techniques such as restriction enzymes are needed to be handled in the laboratory as it is easier and to obtain multiple copies for analysis and manipulation. Recombinant DNA technology has multiple applications in many fields, such as agriculture, archaeology, biological and medical research, and forensic science. The chapter shows how genome editing using the CRISPR-Cas9 system is a powerful new technology that allows precise changes to be introduced into genome sequences.
The Growth, Measurement, and Visualization of Cells
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter looks at the growth, measurement, and visualization of cells which has been achieved with the help of laboratory techniques and equipment. A good aseptic technique is crucial as it enables researchers to work safely with protection and limits the contamination of cultures with unwanted microbes. Microbial culture collections represent a community of isolated microbes from a particular environmental niche and are subsequently grown in the laboratory to allow the individual species present to be identified and be studied in more detail. The chapter mentions how the ability to culture eukaryotic cells in vitro helped develop our current understanding of cell biology. It explains how cell growth can be described through growth kinetics.
Reproductive System
Authors: Scott Jon , Cameron Gus , Goodenough Anne , Hawkins Dawn , Koenig Jenny , Luck Martin , Papachristodoulou Despo , Snape Alison , Yeoman Kay , Goodwin Mark
Published: September 2023

This chapter focuses on the reproductive system. It acknowledges reproduction as a core physiological process that enables diversity and the continued existence of human life. The sexual reproduction cycle consists of a series of stages: gamete production, fertilization, pregnancy, birth, and puberty. The chapter also considers the differences between male reproductive anatomy and female reproductive anatomy by noting their respective features and functions. It details that the activities in the gonads are regulated by the hormones released by the hypothalamus and anterior pituitary (the hypothalamic-pituitary axis). Meanwhile, the monthly cycle in the mature female involves both the maturation and release of the oocyte, and the preparation to facilitate fertilization.
Transcription
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter addresses transcription, which is a key step in gene expression. In order for the information in the genome to be expressed, the cell must synthesize an RNA copy of the DNA. The RNA polymerase enzyme catalyses the synthesis of the RNA from ribonucleotide triphosphate precursors, using the DNA template strand to assemble a copy of the coding strand. RNA is synthesized from the 5' to the 3' end in a defined series of events known as the transcription cycle: initiation, elongation, and termination. Transcription begins with isomerization of RNA polymerase to form the open complex, in which the DNA strands are separated and synthesis of the RNA begins, using the template strand to position the incoming ribonucleotide triphosphates. RNA polymerase may first go through several cycles of abortive initiation, producing very short transcripts, before breaking free of the promoter and entering into the elongation phase.
Biological macromolecules: the infrastructure of life
Authors: Crowe Jonathan , Bradshaw Tony
Published: September 2023

This chapter studies some of the key biological macromolecules that make life happen: amino acids and proteins, nucleic acids, carbohydrates, and lipids. Amino acids join together to form polymers named polypeptides. The structure of proteins is built up over four levels of hierarchy: primary, secondary, tertiary, and quaternary. Protein structure is stabilized by both non-covalent interactions (including hydrogen bonds and hydrophobic interactions) and covalent bonding, including disulfide bonds. The chapter also describes the two key natural nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are polymers of nucleotides. The chapter then considers the three main classes of carbohydrate (sugar)—monosaccharides, disaccharides, and polysaccharides. It also looks at the three most important types of lipid: steroids, triacylglycerols, and the glycerophospholipids.
Preparing scientific presentations
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter focuses on scientific presentations. The ability to present information verbally to a group of people is an increasingly important skill for students undertaking bioscience degrees. It is also one of the key skills that many employers look for across a wide range of roles. This chapter begins by considering the purpose of presentations as a form of assessment. It then identifies some of the characteristics of effective presentations—scientific presentations in particular. The chapter looks at the importance of finding out the answers to a number of key questions before progressing on to analysing the brief, researching the topic, and planning and ordering the presentation’s content. Finally, this chapter highlights the importance of preparing effective and appropriate notes.
Introduction: development of methods and concepts in organic stereochemistry
Authors: Robinson Michael J.T.
Published: September 2023

This chapter introduces the development and benefits of organic stereochemistry. It offers a brief survey of the history of organic stereochemistry to about 1960 and presents many of the more important terms used in organic stereochemistry. The chapter opens with the discussion about shapes of molecules and
optical activity
in organic liquids which was taken by Fresnel. It also explores Pasteur’s recognition of
enantiomerism
in tartaric acids–emphasizing the three known tartaric acids. Towards the end, the chapter turns to explanations by Van't Hoff and Le Bel of the existence of pairs of enantiomeric molecules. It also looks at the two notable lactic acids, which come from milk and from muscle. It concludes by presenting some reaction sequences and explores the study of organic reaction mechanisms.
Introduction to Bioinformatics
Authors: Lesk Arthur M.
Published: September 2023

Introduction to Bioinformatics starts off by introducing the topic. It then looks at genetics and genomes. It moves on to consider the panorama of life. The text also considers alignments and phylogenetic trees. There is a chapter on structural bioinformatics and drug discovery. The text also examines scientific publications and archives, particularly media, content, access, and presentation. Artificial intelligence is considered as well, in addition to machine learning. There is an introduction to systems biology that follows towards the end. The book's final chapters look at metabolic pathways and control of organization.