bluuebunny/crossref_metadata_2025 huggingface dataset:
The structures of simple solids
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter looks at the structures adopted by ions in simple solids and explores why one arrangement may be preferred to another. It starts with the simplest model, in which atoms are represented by hard spheres and the structure of the solid is the outcome of stacking these spheres densely together. This close-packed arrangement provides a good-description of many metals and alloys and is a useful starting point for the discussion of numerous ionic solids. The chapter also considers some of the energy considerations that can be used to rationalize the trends in structure and reactivity. Lastly, it discusses the electronic structures of materials through the extension of molecular orbital theory to the almost infinite arrays of atoms found in solids with the introduction of the band theory.
Acids and bases
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter focuses on the wide variety of species that are classified as acids and bases. It first explains the Brønsted -definition, in which an acid is a proton donor and a base is a proton acceptor. The discussion on the characteristics of Brønsted acids covers the periodic trends in aqua acid strength, simple oxoacids, anhydrous oxides, and polyoxo compound formation. The chapter also introduces the Lewis definition of acids and bases which deals with reactions involving electron-pair sharing between a donor (the base) and an acceptor (the acid). This broadening enables the extension of the discussion on acids and bases to include species that do not contain protons and reactions in nonprotic media. Furthermore, the chapter introduces a molecular orbital description of hydrogen bonding. Lastly, it discusses the nonaqueous solvents and -describes some of the most important applications of acid–base chemistry.
The Group 1 elements
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter discusses similarities and trends in the properties of the Group 1 elements, also called alkali metals. This group includes lithium, sodium, potassium, rubidium, caesium (cesium), and francium, which have low densities and are very reactive. The latter, however, is not discussed as it exists naturally only in minute quantities and is highly radioactive. The chapter provides information about these metals’ occurrence and extraction, and uses and compounds, including the atypical properties of lithium. It also discusses the trends in the properties of the simple binary compounds in terms of the ionic model and the nature of complexes and organometallic compounds of the elements.
The Group 13 elements
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter focuses on the occurrence and isolation of each element in Group 13. This shows a wide variation in abundance in crustal rocks, the oceans, and the atmosphere. The chapter considers the chemical properties of the elements and their simple compounds, coordination compounds, and organometallic compounds. The chapter describes the diverse physical and chemical properties of boron, aluminium, gallium, indium, and thallium. Aluminium is the most important element commercially and is produced on a massive scale for a wide range of applications requiring a strong light metal. Boron forms a large number of cluster compounds involving hydrogen, metals, and carbon. Gallium and indium in alloys and compounds have important electronic and optical properties. The chapter looks at the hydrides, trihalides, and sulfides of some of these elements. Furthermore, it tackles the compounds with Group 15 elements and the Zintl phases.
The d-block elements
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter focuses on the d-block elements, which are all metallic and which have chemical properties crucial to biology, industry, and many aspects of contemporary research. This includes the Group 3 to Group 12 elements. The chapter concentrates on specific properties of the individual elements and some of their important compounds. It describes their occurrence and recovery, highlighting that the chemically soft members of the block occur as sulfide minerals and some can be roasted in air to obtain the metal; and the more electropositive hard metals occur as oxides and are extracted by reduction. The chapter also briefly explains how metal-metal bonds arise and why mercury is toxic.
d-Metal organometallic chemistry
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter takes a closer look at the organometallic chemistry of the d metals. It starts by looking at the d-block organometallic compounds that were synthesized and partially synthesized in the nineteenth century. The chapter also discusses the bonding of d metals, including stable electron configurations, electron count preference, electron counting and oxidation stages, and nomenclature. It also tackles ligands in some detail in relation to d metals. It specifically looks at carbon monoxide, phosphines, hydrides, and dihydrogen complexes, among others. Then it considers the structures, bonding, and reactions of metal carbonyls, which historically formed the foundation of much of d-block organometallic chemistry. Lastly, the chapter looks at the reactions of a large variety of organic ligands and relevant catalysis.
Materials chemistry and nanomaterials
Authors: Weller Mark , Rourke Jonathan , Overton Tina , Armstrong Fraser
Published: September 2023

This chapter discusses materials chemistry, focusing on solid-state compounds, their synthesis, structure, and electronic, magnetic, and optical properties. Important applications of these solid materials include optoelectronics, renewable energy generation and storage, and heterogeneous catalysis using porous materials. The chapter describes how inorganic materials are synthesized as bulk solids. It shows the important role of defects in controlling the properties of solids, including ion migration. Then it focuses on key classes of inorganic materials, including intercalation compounds, photovoltaics, and photocatalysts, complex electronic oxides, magnetic compounds, framework structures, and their use as heterogeneous catalysts, pigments, and molecular materials. The discussion in the chapter also touches on nanomaterials chemistry, an area that has developed enormously in the past decade.
Sample Preparation
Authors: Warford Anthony , Hing Sandra
Published: September 2023

This chapter looks into the preparation of samples. It explains the process of degrading cells and tissues after the removal of nutrients and the supply of oxygen. Additionally, the chapter lists the different types of samples suitable for genomic analysis and proteomic analysis. It discusses how to optimally prepare and store samples, which depends on what the analytical destination will be. All samples degrade due to the impact of ischaemia, leading to autolysis and putrefaction if the sample is in a non-sterile environment. The chapter also explores various methods used to establish the quality and quantity of samples of DNA, RNA, and protein.
Intact Sample Analysis
Authors: Warford Anthony , Volpi Emanuela V.
Published: September 2023

This chapter focuses on intact sample analysis. It explores the technologies used in analysing nucleic acids and proteins in intact samples, either as single cells or tissues. The chapter also discusses the validation of antibodies for protein analysis and nucleic acid probes for the visualization of DNA and RNA. Moreover, it highlights the development, principles, key technical considerations, and procedures of immunocytochemistry, flow cytometry, and in situ hybridization for the demonstration of proteins and nucleic acids. While immunocytochemistry and in situ hybridization share many procedural similarities and can be undertaken manually or using automated platforms, flow cytometry is a quantitative automated technique.
Sequencing Technologies
Authors: Presneau Nadège , Hamoudi Rifat
Published: September 2023

This chapter explores the technologies used for sequencing. It discusses the principles of first-generation sequencing, namely Sanger sequencing and pyrosequencing methods. The chapter also notes the principles of sequencing by synthesis (SBS) alongside the technologies developed for second-generation sequencing, that is, Illumina and Ion Torrent. Additionally, it discusses third-generation sequencing, which allows the real-time sequencing of single molecules, and the fourth-generation sequencing, which merged in situ cellular localization and gene expression sequencing. The chapter then highlights the main advantages and challenges associated with each sequencing technology and considers some of their applications.
Molecular Analysis and Interpreting Molecular Data
Authors: Hamoudi Rifat , Warford Anthony
Published: September 2023

This chapter focuses on molecular analysis and interpreting molecular data. It looks at the types of data generated from homogenate and intact cell and tissue preparations and considers how these could be analysed through qualitative, semi-quantitative, and quantitative methods. Moreover, the chapter explores bioinformatics as an answer to the interrogation of DNA and RNA target sequences, epigenetic changes, and DNA-protein relationships. It provides an overview of the application of telepathology, and image capture and analysis to achieve diagnosis without requiring microscopy. Finally, the chapter highlights the significance of developing sophisticated bioinformatics algorithms in an effort to correlate data from various sources with clinical pathology data in order to aid the diagnosis of disease and patient management.
Recent Technical Advances in Molecular Analysis
Authors: Presneau Nadège , Alikian Mary
Published: September 2023

This chapter explores the recent technical advances in molecular analysis. It discusses the science and development behind liquid biopsy and digital PCR. The chapter defines liquid biopsy as a minimally invasive procedure used for screening, diagnosis, prognosis, and predictive testing of circulating biomarkers. It regards liquid biopsy as the future of precision medicine. Digital PCR is identified as a highly precise analytical technique for nucleic acids' absolute quantification based on PCR amplification of a single template molecule without the need for a calibration curve. The chapter also includes a range of clinical applications using digital PCR and liquid biopsy.
Mesenchymal Tumours
Authors: Amary Fernanda
Published: September 2023

This chapter focuses on mesenchymal tumours. It defines mesenchymal tumours as relatively common neoplasms derived from cells of the mesenchyma: bone, muscle, fat, and connective tissue. The chapter considers the genetic abnormalities found in mesenchymal tumours. It discusses the application of molecular diagnostic assays in clinical scenarios of diagnosing and treating mesenchymal tumours by referencing chromosomal translocations, gene rearrangements, gene amplifications, and point tumours. Additionally, the chapter includes the most common abnormalities in the main sarcoma subtypes, which are regarded as rare malignant mesenchymal tumours with complex and diverse histological subtypes. It clarifies that benign tumours are usually not life-threatening and can be treated with simple excision.
The Boltzmann law
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

This chapter looks at the Boltzmann law with respect to the concept of classical thermodynamics. It stresses that thermodynamics is based on three laws of experience. The chapter discusses the Boltzmann factor wherein the unit, energy per unit of temperature, is needed to make the exponent dimensionless. It explores the average basis of matter behaviour. Additionally, certain aspects of the laws of probability are used to establish assumptions and understand the Boltzmann law. The chapter briefly discusses these aspects, including distinct and independent particles, configurations of sharing energy, statistical weights, equal probability of configurations, conservation of number and energy, and maximization subject to constraints.
Thermodynamic functions: towards a statistical toolkit
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

This chapter explores thermodynamic functions as a statistical toolkit. It refers to state functions as major thermodynamic variables. The two thermodynamic functions most usually chosen as the basis for variables are the energy E—leading to the internal energy U—and entropy S. The chapter highlights that the Massieu bridge will form the basis of all of the other thermodynamic functions needed. It notes that the pressure is related to the Helmholtz free energy through the first derivative in relation to volume at a constant temperature. The chapter considers the relation between internal energy, heat capacity, entropy, enthalpy, and Gibbs free energy, which is linked with Helmholtz free energy. The chapter shares the full set of toolkit equations which can be used in the field of thermodynamics.
The ideal diatomic gas: the rotational partition function
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

This chapter looks at the ideal diatomic gas in relation to the rotational partition function. It explains how rotational motion is restricted to certain values of the available energy, and molecules thus have access to a manifold of quantized rotational energy levels. The chapter discusses rigid rotor assumptions and continuum approximation as a test of validity. Heteronuclear diatomic molecules do not have a symmetry and must rotate through 360° before reaching an indistinguishable state. However, it is important to recognize the existence of rotational indistinguishability for symmetrical molecules. Additionally, the chapter looks at the origin of the symmetry factor. It uses equation diagrams of the standard toolkit functions to look into rotational energy, heat capacity, and entropy.
ortho and para spin states: a case study
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

This chapter explores the ortho and para spin states. It explains how ortho states are linked with symmetric nuclear spin wave functions, while para states are linked with antisymmetric nuclear spin wave functions. The chapter notes the ortho and para spin states of hydrogen as well. Additionally, it looks at the special case of nuclei with zero spins. Nuclear spin energy states are very closely spaced in energy and have small nuclear spin temperature characteristics; thus only hydrogen and its isotopes at a lower temperature experience a change in the equilibrium orientation of nuclear spin. The chapter highlights the main influence of nuclear spin that defines the statistical weights of rotational states in symmetrical molecules.
The electronic partition function
Authors: Maczek Andrew , Meijer Anthony
Published: September 2023

This chapter focuses on the electronic partition function. Atoms and molecules can achieve electronic excitation energy levels and experience a rise in energy to states above the ground electronic state. The chapter highlights that excited electronic states showcase no regular or predictable series of increasing energies. It notes that high excitation energies mean that molecules' excited electronic states remain unpopulated unless the temperature increases to several thousands of kelvins. Additionally, the chapter includes degeneracy in the equation formula as electronic states can enter into the partition function for atoms via the degeneracy of the ground electronic state. The chapter explores the singular case of nitrogen monoxide as an isolated two-state system.
Properties of Aliphatic Hydrocarbons
Authors: Hall Andrew J.
Published: September 2023

This chapter details how molecules that have short or long chains or more complicated arrangements of carbon atoms can be produced. Hydrocarbons are compounds made solely of carbon and hydrogen atoms, in which each carbon forms four covalent bonds. The chapter highlights the importance of hydrocarbons in everyday lives as they are a source of energy used to heat and light homes, power vehicles, and provide many of the plastic items being used. The chapter talks about the abundance of hydrocarbons in nature, such as flavours or fragrances produced by plants, insect pheromones, and natural rubber and lipids. It explores the properties of the aliphatic hydrocarbons: the alkanes, alkenes, and alkynes.
Lipids
Authors: White Alex , Burrell Helen
Published: September 2023

This chapter deals with the final class of macromolecules: lipids. Lipids possess a greater variety of structural types than the previous classes of macromolecules and include fatty acids, triglycerides, phospholipids, and steroids. The chapter defines lipids as water-insoluble molecules which stem from biological systems that are readily soluble in non-polar organic solvents. The chapter analyzes the non-polar properties of lipids which are vital to several important aspects of their biochemical roles and differ from the macromolecules as they do not form large polymeric structures. Fatty acids are the best-known examples of lipids, though they are usually found in biochemistry as components of larger molecules.
Describing Data
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 how to describe collected data and it examines the continuous scale level. It explores the calculation of mean, median, and mode as measures of central tendency. Frequency distribution illustrates the central tendency, shape, and variability of data based on observation rather than theory. Meanwhile, theoretical frequency distribution is a type of data description that can be generated by a mathematical equation. The chapter considers three theoretical distributions useful to biologists: the normal, Poisson, and binomial distributions. It also cites the importance of describing the variability of data and central tendency by explaining how to measure variability through range, interquartile range, variance (s2), and standard deviation (s).
Microbes in 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 tackles the involvement of microbes in the production of pharmaceutical drugs, food, and drinks. It defines biotechnology as the use of any living organism in an industrial process for reasons such as easier cultivation and genetic manipulation. Moicrobes play a role in the treatment of waste material through the use of biological control agents and in bioremediation. The chapter also highlights the essential role of microbes in all biogeochemical cycles as they enact the chemical transformation of elements. A biogeochemical cycle encapsulates the processes involved in cycling an element through various biological, chemical, and geological forms in air, water, and soil systems.
Populations
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 population with reference to the quantification of demographics and modelling changes. It cites the key demographic factors of population demographics, which are population size, population density, population distribution, population dispersion, and population structure and life-history parameters. Population data can be collected in several ways, each one depends on the subject's species, environments, and the study's purpose. The chapter explains that the ability to understand, quantify, and model changes in the size of a population is vital to the study of population ecology and the subsequent practical management of endangered populations. It also tackles the traits to be considered when modelling life-history strategies.
Ecosystems
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 notions of abiotic interactions and environmental processes concerning ecosystems. Ecological communities interact with their environment in ecosystems through processes, such as photosynthesis, energy exchange, and nutrient cycling. The chapter cites the interchangeable notion of biomes and ecosystems, and notes how both terms differ in the scale they both cover for each species. Ecosystem processes involve anything that relates to energy generation and transfer or movement and storage of chemical compounds. The chapter notes the significant role of autotrophs as the power powerhouses of the ecosystem. It also clarifies that mass extinction events occur when there is a catastrophic loss of many species within a very short period.
Assessing Patterns
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 using graphs to display visual data helps the understanding and exploration of data and allows people to make an initial assessment of potential patterns. Frequency distribution graphs are visual depictions of frequency distributions involving just one variable and are used to describe a single sample. The chapter also considers the features and functions of other types of graphs, such as scatterplots. It discusses the implications of sample error within descriptive statistics and graphs. Due to the expansion of computing capacity and technology, biological scientists today have a wide range of analytical techniques available to them.
Using Formulas and Equations
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 a number of features of formulas and equations. It starts with the anatomy of an equation, and notes how symbols signify operators and letters can stand for variables or constants. Keeping track of the units in a calculation is very important. The chapter also examines generic forms of equations commonly used in biology and the rearrangement of formulas through addition, subtraction, multiplication, square root, and logs. It shows how exponential growth equations can be used in a number of biological situations, such as the growth of bacteria, cells, and animals.
Proteins and Proteomes
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, features, and function of proteins. It cites amino acids as the building blocks of proteins. Proteins carry a range of functions, such as the agents of biochemical reactions of cellular metabolism or hormones transmitting signals from one cell to another. The chapter then details the four levels of protein structure that are dependent on polypeptide chains. Enzymes function as biological catalysts that make a chemical reaction more likely to occur and speed up the overall rate. The chapter acknowledges how modern protein technology methods allow the rapid identification of proteins and the growth of proteomics as a field of study.
Characteristics of Prokaryotic and Eukaryotic 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 explains the characteristics of prokaryotic and eukaryotic cells. It starts by looking at the diversity of cells before moving on to talk about the characteristics of the Bacteria and Archaea. Cells were first identified through the phospholipid membrane, which is common to all life. Even though all the cells in any one organism share the same genetic material in their nuclei, they are not identical as specialized cells undertake specific functions as a result of cell-specific gene expression and consequent protein production. Specialist cells come together to form organs and tissues, mediated by interactions between different cells and between cells and the extracellular matrix.
Cell Division in Prokaryotes and Eukaryotes
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 cell division in prokaryotes and eukaryotes. Life on Earth depends on cell division and the transfer of genetic information which triggers the propagation and evolution of species. Unlike the reproduction of eukaryotes, prokaryotes adopt asexual reproduction strategies such as binary fission, budding, or fragmentation. The chapter provides an overview of the process of mitosis wherein one single cell divides to produce two genetically identical daughter cells. Meiosis is a special form of cell division that occurs during the formation of gametes. The chapter explains the process of meiosis involving the production of haploid gametes for sexual reproduction of eukaryotic organisms.
An Overview of Physiology
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 physiology while focusing on human physiology. It highlights the importance of understanding physiology for medical science as physiology reflects the conscious perception of the internal and external world. Homeostasis primarily refers to the maintenance of the internal environment within very tight boundaries, which underpins the exploration of physiology. Homeostasis relies on a variety of sensory systems that detect changes and initiate responses to oppose changes such as negative feedback. The chapter also notes the cell membrane as a fundamental structure to consider in physiology, citing its role as a barrier that regulates the flow of substances in and out of the cell.
Genomes and the flow of biological information
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter provides an overview of genomes and the flow of biological information. Biological information is typically stored in the nucleic acid DNA referred to as the genome. A gene is typically defined as a region of DNA that controls a discrete hereditary characteristic. The first stage of gene expression is transcription, in which an RNA copy of the gene is synthesized. Messenger RNAs (mRNAs) are then translated to produce a protein product in a process mediated by the ribosome. The regulation of gene expression in both time and space is extensive and occurs at every level of expression. The chapter then looks at cellular infrastructure and gene expression. The overall expression of an organism's genome determines its phenotype—that is, its physical features and properties. The chapter also assesses the evolution of the genome and the tree of life, considering the process of natural selection.
Biological molecules
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter reviews how molecules are built up by linking atoms together with covalent bonds and explores the way in which molecules interact with one another non-covalently in the aqueous environment of the cell. There are four major classes of biological molecules that play essential roles in all organisms: nucleotides, amino acids, carbohydrates, and lipids. Each of them can be found in cells both as individual small molecules or covalently linked to form larger molecules known as polymers or macromolecules. Nucleic acids are polymers of nucleotides that are responsible for carrying genetic information. Proteins, on the other hand, are polymers of amino acids that function as workhorses, carrying out most of the chemical reactions in the cell and giving cells their structure and shape. Many biological molecules can be covalently modified in ways that alter their chemical properties and allow their function to be regulated.
The chemical basis of life
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter discusses how enzymes catalyse chemical reactions and how enzyme activity is regulated in the cell. The behaviour of molecules in living cells is governed by the laws of chemistry and physics. The thermodynamic and kinetic principles underlying chemical reactions in the cell can be used to describe biological processes and predict how cells will respond to different conditions. The chapter then shows how to apply these principles to understand and predict binding interactions and enzyme catalysis. Enzymes catalyse reactions by lowering the activation energy barrier through a variety of strategies. These include binding preferentially to the transition state of the chemical reaction and binding simultaneously to two substrates, orienting them favourably for reaction. Many enzymatic reactions obey Michaelis–Menten kinetics.
DNA replication
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter evaluates DNA replication, which occurs in three distinct phases: initiation, elongation, and termination. Initiation of replication in bacteria occurs at a unique chromosomal location called an origin, which is recognized by specific proteins. Initiation of replication in eukaryotes, in contrast, usually occurs stochastically at sites marked in the genome by binding of the pre-replication complex. New DNA strands are initiated by RNA or combined RNA and DNA primers, which are synthesized by primase in bacteria and the polymerase α-primase complex in eukaryotes. After their initial synthesis, the primers are then elongated by the replicative DNA polymerase. The termination of replication occurs when two replication forks traveling in opposite directions meet. The chapter then looks at the regulation of the initiation of DNA replication, the end-replication problem, and the replication of chromatin.
Regulatory RNAs
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter highlights regulatory RNAs. RNA molecules can act as regulators by base-pairing with target RNAs or even DNA, or by binding metabolites or proteins, to block or facilitate the binding of other RNAs or proteins and bring molecules into proximity. Most base-pairing RNAs in bacteria are expressed in response to specific environmental conditions. The chapter then looks at microRNAs (miRNAs), small interfering RNAs (siRNAs), and Piwi-interacting RNAs (piRNAs). miRNAs are encoded by distinct genes and modulate translation and mRNA destabilization. siRNAs are generated through excision along the length of a double-stranded RNA of either external origin or endogenous origin and direct RNA interference and transcriptional silencing. Meanwhile, piRNAs are derived from repetitive regions of the genome, are associated with Piwi family Argonaute proteins, and repress the expression of diverse repeat sequences in the nucleus. The chapter also considers the viral defense role of CRISPR systems.
Protein modification and targeting
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter reviews protein modification and targeting. Protein chaperones assist in the proper folding and unfolding of proteins by interacting with hydrophobic regions of the protein. Some proteins require the formation of disulfide bonds for their correct folding. Meanwhile, proteins are targeted to specific subcellular locations by amino acid sorting motifs, as well as by the attachment of lipids such as fatty acyl groups, isoprenoid groups, or GPI (glycosylphosphatidylinositol) anchors. The chapter then looks at post-translational cleavage. Some proteins need to be cleaved by site-specific proteases before they are active, while other proteins contain self-excising inteins, which must be removed from the protein product for it to become active. The chapter also considers covalent modification of proteins, including lipid modifications, before assessing protein degradation.
Tools and techniques in molecular biology
Authors: Craig Nancy L , Green Rachel , Greider Carol , Storz Gisela , Wolberger Cynthia , Cohen-Fix Orna
Published: September 2023

This chapter explores tools and techniques frequently used in molecular biology. Molecular biology methods range from genome-wide analysis to the dissection of interactions between isolated single molecules. A key aspect of molecular biology is the study of processes both in vivo and in vitro. The chapter begins by describing the organisms that have served as models for the study of biology in all types of cells and studies how cells and viruses can be grown in culture. It then looks at genome manipulation and genome sequencing, as well as cellular imaging and molecular structure determination. The chapter considers the amplification and cloning of nucleic acids and how such cloning, known as recombinant DNA technology, can be used both to identify new genes and to construct modified genes and chromosomes.
Introduction
Authors: McCullagh James , Oldham Neil
Published: September 2023

This chapter explains that mass spectrometry (MS) is an analytical technique that forms ions from atoms or molecules and measures their mass-to-charge ratios. It points out how MS provides information about molecular and elemental composition and quantifies the abundance of individual chemical components. It also deals with ions which can be accelerated, deflected, and deaccelerated in electric and magnetic fields. These are crucial features for the operation of a mass spectrometer. The chapter emphasizes the formation of a molecule into a gas-phase ion which should be stable long enough to reach the detector of the mass spectrometer. It discusses the important part of the history of MS, which is the development of instrumentation that is capable of measuring compounds with a wider range of chemical and physical properties.
Interpretation of mass spectra
Authors: McCullagh James , Oldham Neil
Published: September 2023

This chapter describes the resulting fragmentation pattern seen in the mass spectrum or MS/MS spectrum, which can be used to provide information about the structure of the molecule. It explains how fragmentation data can be interpreted and outlines the fragmentation of small organic molecules using EI-MS. It also introduces the basic types of fragmentation process and presents the diagnostic ions and neutral losses seen for different organic structures and functional groups. The chapter summarize the dissociation of protonated and deprotonated molecules ([M+H]+/[M–H]-), such as those formed by ESI, MALDI, or CI. It discusses the fragmentation of small molecules, including peptides and other large biomolecules.
Mass spectrometry applications
Authors: McCullagh James , Oldham Neil
Published: September 2023

This chapter reviews the ability of mass spectrometry (MS) for identifying and quantifying individual compounds from complex samples with high sensitivity. This has led to a wide range of physical, chemical, biological, medical, and industrial applications. It cites examples that have benefited from technical advances in sensitivity, selectivity, and the ability to process mass spectrometric data more rapidly and at a larger scale. It also points out how developments in MS have enabled the identification and quantification of proteins and metabolites in biological samples and metabolomics. The chapter deals with small molecule applications, particularly those related to the environment, sports, biology, and medicine. It focuses on the characterization of larger molecules with an emphasis on the analysis of proteins and mass spectrometry imaging.
Potentials, interfaces, electrodes, and mass transport
Authors: Browne Wesley R.
Published: September 2023

This chapter looks into potentials, interfaces, electrodes, and mass transport. It presents dynamic and static categorization of electroanalytical methods. The chapter then explores the surface of an electrode. Following from this, the chapter explains the process behind electrode polarization and electrode potentials. It notes the consequences of differences in the concentrations of electrolytes in pairs of half-cells by referencing transference numbers and the transfer of ions across a phase boundary and liquid junction potentials. The chapter shows how indicator electrodes are commonplace in laboratories and make use of ion-selective membranes. The chapter notes the measure of the concentration of species in particular oxidation states. This is called potentiometry. The chapter also describes diffusion, convection, and shows that migration is the phenomena of mass transport at an electrode.
Molecular interactions: holding it all together
Authors: Crowe Jonathan , Bradshaw Tony
Published: September 2023

This chapter evaluates non-covalent interactions, which operate between parts of one molecule (intramolecular) or between separate molecules (intermolecular), and which are primarily electrostatic in nature, and operate over only short distances. The chapter also looks at polarization, the process by which electrons are unevenly distributed within a molecule, before explaining the van der Waals interaction—the overall interaction between two species once both attractive and repulsive interactions are taken into account. The chapter then considers dispersion forces, permanent dipolar interactions, induced dipolar interactions, and steric repulsion. It studies other biologically essential interactions, including hydrogen bonds, ionic forces, and hydrophobic forces. Finally, the chapter examines how molecular interactions influence water solubility, before outlining the three phases of matter: solid, liquid, and gas. It also identifies the transitions between phases, including melting, vaporization, condensation, solidification, sublimation, and deposition.
Moles, concentrations, and dilutions: making sense of chemical numbers
Authors: Crowe Jonathan , Bradshaw Tony
Published: September 2023

This chapter details the language of measuring chemical quantities, focusing on one quantity in particular: the mole. The mole is a convenient way of scaling down large numbers: one mole of atoms represents 6 × 1023 atoms. The molar mass is the mass of one mole of a substance. The concentration of a solution tells us how much of a substance is present in a particular volume of that solution. When preparing solutions according to percentage by weight, one uses a mass of substance that equates to a certain percentage of the volume of the final solution. The chapter then looks at dilutions, explaining how the number of moles of the solute remain the same after dilution, but the total volume increases, so the concentration decreases. The chapter also highlights some of the tools for measuring concentrations, including titrations, UV-visible spectroscopy, atomic emission spectroscopy, and fluorescence spectroscopy.
Acids, bases, and buffer solutions: life in an aqueous environment
Authors: Crowe Jonathan , Bradshaw Tony
Published: September 2023

This chapter discusses the key properties of aqueous environments that are pivotal to biochemical reactions happening correctly. It examines the behaviour of acids and bases—why they are important to the chemistry of life, what distinguishes them from other compounds, and how their behaviour is kept in check. The chapter outlines the Brønsted–Lowry definitions of acid and base: namely, that an acid is a hydrogen ion donor, while a base is a hydrogen ion acceptor. The chapter then looks at conjugate acid–base pairs, before considering the strength of acids and bases. The acid dissociation constant provides a measure of the extent to which an acid dissociates in aqueous solution. The chapter also studies the ion product of water, the pH scale, and neutralization reactions. It also discusses the behaviour of acids and bases in biological systems before turning to buffer solutions, and their importance to biology.
Chemical analysis: characterizing chemical compounds
Authors: Crowe Jonathan , Bradshaw Tony
Published: September 2023

This chapter explores chemical analysis—the process of characterizing chemical compounds. It begins by looking at separation techniques, including solvent extraction, chromatography, electrophoresis, and centrifugation. The chapter then considers the use of mass spectrometry in determining the mass of a compound in a sample. It also outlines different spectroscopic techniques, which use the behaviour of compounds when they interact with electromagnetic radiation to help characterize them. Different spectroscopic techniques use different parts of the electromagnetic spectrum to ask different questions about chemical structure. These spectroscopic techniques include nuclear magnetic resonance (NMR) spectroscopy, infrared spectroscopy, and UV–visible spectroscopy. Finally, the chapter discusses X-ray crystallography, which reveals the three-dimensional structure of a compound in crystalline form.
Writing essays
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter discusses essay writing. Essay writing is a very common form of assessment in almost all degree courses in the biosciences, both as coursework and for examinations. For many students, however, writing essays at university represents a real challenge, as it is a skill that is only developed to a limited extent in pre-university courses. This chapter thus goes through the process of planning and writing scientific essays. It shows the importance of planning time to avoid rushing at the last minute; analysing the question or title carefully; researching the topic carefully, using the different sources available; planning the structure and order of the essay; reviewing, redrafting, and proofreading to make sure the question has been answered, that the structure is logical, that the citations and references are correct, and that there are no spelling or grammatical mistakes.
Working in tutorials and groups
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter focuses on tutorials and group work. These form key elements of teaching within most degree programmes and can be employed in a variety of formats. Irrespective of the specific format of a session, the most important things that can be done for tutorials and group work are to prepare and to participate. Preparing for academic tutorials means reading through any lecture notes or reference material to understand the subject well beforehand. During the tutorials, the student must listen to what others have to say and be prepared to take their ideas on board, as well as argue against them if necessary. For group work, the student must be prepared to work with other people, personal feelings aside. The chapter emphasizes that the group members must keep meeting regularly and checking progress against their timeline.
Delivering scientific presentations
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter is devoted to the delivery of scientific presentations. It expands on the previous chapter’s topic by demonstrating how to effectively communicate content. Communicating the content involves a very different set of skills to preparing the content, hence why it is important to develop the skills to communicate content effectively. The chapter begins by highlighting common concerns people have about presentations and how to address them. Written and spoken presentations are differentiated here. Next, it considers how to use visual aids effectively and appropriately so as to keep them from becoming too distracting. And finally, the chapter provides some key techniques to help one’s presentations run smoothly.
Getting the most out of exams
Authors: Stuart Johnson , Jon Scott
Published: September 2023

This chapter address the skills a student needs for taking exams. It emphasizes that exam skills are not just needed during exams; there are some important exam skills that need to be developed for the days leading up to exams, as well. What the student does just before an exam, and when they arrive in the exam room, are important stages of exam preparation. With this in mind, the chapter begins by addressing what needs to be done immediately before exams, and then progresses to give guidance about the exams themselves. Different types of question require slightly different techniques, but, as this chapter shows, all of them require the ability to analyse questions, and to plan, write, and review answers.
Stereoisomerism in molecules and compounds
Authors: Robinson Michael J.T.
Published: September 2023

This chapter emphasizes the classification of
isomerism
and then goes on to an account of stereoisomerism in molecules and compounds. It argues that classification requires nomenclature–adding that stereochemistry has seen many changes in nomenclature and these are still developing. The chapter seeks to give an adequate but not pedantic account of current nomenclature. It begins with the definition of stereochemical nomenclature, then proceeds to review the relationships between the enantiomeric/diastereomeric and enantiomer/diastereomer. Ultimately, the chapter shifts to examine molecules and compounds, especially in terms of molecular structure. It analyzes the detection of chirality in compounds and presents the stereogenic units in molecules.
Paramagnetism – part I
Authors: Orchard A. F.
Published: September 2023

This chapter highlights net paramagnetism observed in open-shell compounds, dominated as a result of electron spin. It mentions free open-shell atoms or ions that have well-defined orbital momentum and examines the nature of the individual spin and orbital components of susceptibility. These depend on the details of coupling in the ground state. It also reviews the applicability of theory and certain discordant data involving ions of the lanthanide elements in their compounds. The chapter discusses paramagnetism observed in the lanthanide and actinide metals and prominent metallic compounds of the lanthanide elements. It reviews the interpretation of bulk susceptibilities, which is the principal source of magnetic moment data.
Experimental methods
Authors: Perkins John
Published: September 2023

This chapter recounts the earliest methods for indicating the presence of radials as intermediates in organic reactions, which include the formation of a polymer when a polymerized monomer is added to the system. It talks about the mechanisms that operate in the reactions with the molecular oxygen of organolithium compounds and Grignard reagents. It also refers to the use of conventional optical spectroscopy. This may be practical for experiments where moderate concentrations of strongly absorbing species are readily attainable. The chapter describes electron spin resonance (ESR) spectroscopy as a sensitive magnetic resonance technique that is considered as an electron counterpart of proton magnetic resonance spectroscopy. It explores the capability of ESR spectroscopy ion providing structural information on paramagnetic species.