This chapter reviews the general functions of hormones, their chemical nature, mechanism of action, and regulation, before focusing on disorders of hormones released by the pituitary gland. Hormones are chemical messengers produced by endocrine glands that circulate in the blood and act on target cells via receptors. The pituitary gland is influenced by release of peptides from the hypothalamus and also releases peptide hormones itself, which influence release of hormones from other endocrine glands located in the thyroid, adrenals, and gonads. The chapter then differentiates between hyperfunction and hypofunction of the anterior pituitary. Posterior pituitary dysfunction can result in low antidiuretic hormone (ADH) secretion, which presents clinically as cranial diabetes insipidus. Release of hormones from the pituitary gland can be investigated by measuring the concentration of single hormones in serum or by dynamic function testing.
Abnormal pituitary function
Abnormalities of lipid metabolism
This chapter explores the role of lipids in the development of cardiovascular disease. Different types of lipids occur in the body and include fatty acids, triacylglycerol, phospholipids, and cholesterol. Lipids are insoluble in water and associate with apoproteins in the blood to give lipoproteins, and this is the form in which they are transported in the circulation. Lipid disorders can either be genetic in origin or secondary to other diseases, drug treatment, or defective nutrition. The chapter then looks at hypercholesterolaemia, hypocholesterolaemia, and hypertriglyceridaemia. Deposition of lipids in arterial walls and the subsequent formation of an atheroma are key features of atherogenesis and coronary heart disease. Management of hyperlipidaemia involves using a combination of lifestyle changes aimed at reducing risk factors and the use of lipid-lowering drugs such as statins.
Academic integrity and avoiding plagiarism
Johnson Stuart and Scott Jon
This chapter explains academic integrity and plagiarism, which is a failure of academic integrity and is an increasing problem. It begins by defining in more detail what plagiarism is. It then looks at some of the reasons students give for plagiarizing in their work. The chapter then outlines a method to avoid plagiarism and highlights some of the many good reasons for doing so. It is important to note that, although most forms of plagiarism probably occur in the context of essays and practical reports, it is possible to plagiarize in any form of communication. As such, this chapter argues that the study skills required to help avoid plagiarism in writing are essential to success in every area of academic work.
This chapter assesses homeostasis of H+ions, the causes and consequences of acid-base disorders, and their laboratory investigation. The physiological control of H+ concentration is maintained by three interrelated mechanisms: buffering systems, the respiratory system, and the renal system. Intracellular and extracellular buffering systems, such as bicarbonate and haemoglobin, provide an immediate, but limited, response to pH changes. The respiratory system, which can be activated almost immediately, controls PCO2 by changing alveolar ventilation. The renal system regulates [HCO3 -] and is the slowest to respond. The physiological response to an acid-base disturbance, which limits the change in H+ concentration, is referred to as compensation. The chapter then looks at acidosis, alkalosis, and mixed acid-base disorders. Acid-base data can be interpreted in a systematic manner, from laboratory results, by examining pH status, PCO2 results, and the compensatory response by HCO3 -.
Acids, bases, and buffer solutions: life in an aqueous environment
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.
Adaptation and Evolved Design
This chapter describes how both functional utility and ancestry contribute to adaptation and the evolved design of organisms. Evolved structures, unlike fabricated structures, are constrained by their origin as modifications of an ancestral state. Hence, structures in two species may be similar in form not because they operate in a similar fashion, but because their common ancestor had the corresponding structure. Characters that are similar among species because they are inherited from the common ancestor of the group are said to be homologous. The central principle of independent evolution leads to the recognition of homology at different phylogenetic levels. The chapter then looks at how evolutionary engineering combines utility and ancestry.
This chapter evaluates the morphology, development, functions, and regulation of the adrenal glands, before looking at adrenal disorders. The adrenal glands have an outer cortical region and an inner medulla with different functions. The adrenal cortex produces aldosterone, cortisol, and dehydroepiandrosterone sulfate (DHEAS); the medulla produces adrenaline and noradrenaline. In the newborn infant, metabolites of DHEAS are also produced by the fetal adrenal gland and can interfere with some methods. The execution and interpretation of laboratory hormone tests need special consideration, particularly with regard to assay specificity, reference ranges for age, development, and in some cases body size. The chapter then considers immunoassays, steroid hormone assays, and the analysis of the profile of urinary steroids by gas chromatography with mass spectrometry. A number of disorders of the adrenal glands are due to genetic defects in enzymes or neoplasms. Once recognized, these disorders are treatable by surgery and/or hormone replacement therapy.
Advanced Probability for Bioinformatics Applications
This chapter starts with the subject of a continuous random variable and then moves to a discussion of the extreme value distribution and its use in analysing the significance of an alignment. It looks into the computation and interpretation of P- and E-values to evaluate sequence alignments. The chapter also discusses the main characteristic of a Markov process (probability of current state dependent only on previous state), then examines how to translate information about a Markov process into a state diagram and the associated transition matrix. It also points out the probability that a particular sequence of states resulting from a Markov process occurs. Next, the chapter analyses the stochastic processes, specifically Markov chains and hidden Markov models, as well as a mathematical derivation of the Jukes-Cantor model.
Aerobic Metabolism I: The Citric Acid Cycle
This chapter discusses modern aerobic organisms that transduce the chemical bond energy of food molecules into the bond energy of adenosine triphosphate (ATP). It examines how aerobic organisms perform this feat where oxygen is used as the terminal acceptor of the electrons extracted from food molecules. The capacity to use oxygen to oxidise nutrients, such as glucose and fatty acids, yields a substantially greater amount of energy than does fermentation. The chapter recounts the accumulation of atmospheric O2 on Earth about 2 billion years ago, when existing organisms were confronted with a serious problem: molecular oxygen forms toxic oxygen ions and peroxides called reactive oxygen species (ROS). ROS react with and damage or destroy biomolecules. Consequently, exposure to O2 acted as a severe selection pressure.
Aerobic Metabolism II: Electron Transport and Oxidative Phosphorylation
This chapter analyses how the aerobic lifestyle depends on the large quantities of energy made possible by oxygen, which is also required directly or indirectly for 1000 biochemical reactions that cannot occur under anaerobic conditions. It cites research efforts which have revealed that aerobic organisms have evolved an array of mechanisms that provide protection from the toxic by-products of oxygen metabolism. Many enzymes and antioxidant molecules prevent most oxidative cell damage. The chapter describes oxygen metabolites that are now known to contribute to an array of human disorders that include cancer and heart and neurological diseases. Oxygen has several properties that, when combined, have made possible a highly favourable mechanism for extracting energy from organic molecules.
Alignments and phylogenetic trees
This chapter examines the concept of sequence alignment, which is the identification of residue-residue correspondences. It is the basic tool of bioinformatics. The chapter presents a comparison of pairwise sequence alignments and multiple sequence alignments. Multiple sequence alignments are much more informative than pairwise sequence alignments, in terms of revealing patterns of conservation. The chapter then looks at the process of constructing and interpreting dot plots, before considering the use of the Hamming distance and Levenshtein distance as measures of dissimilarity of character strings. It also explains the basis of scoring schemes for string alignment, including substitution matrices and gap penalties. Finally, the chapter studies the applications of multiple sequence alignments to database searching, before exploring the contents and significance of phylogenetic trees, and the methods available for deriving them.
All About Sex
This chapter discusses the evolution of sex. Sex refers to copulation and a variety of other mechanisms related to the genes that organisms carry. The chapter then looks into the diverse ways organisms have sex, while also acknowledging that some organisms are asexual and do not need sex to reproduce. It explores female choice and male-to-male competition as modes of sexual selection, which results in the evolution of exaggerated secondary sexual traits that increase mating success but usually decrease survival.The chapter examines how inbreeding depression frequently causes the evolution of mechanisms that prevent self-fertilization and mating between close relatives.
An alternative pathway of glucose oxidation: the pentose phosphate pathway
This chapter examines the pentose phosphate pathway, which is a pathway of glucose oxidation which does not generate adenosine triphosphate (ATP) nor oxidize a molecule of glucose completely. The chapter considers the pentose phosphate pathway as a versatile pathway that produces ribose-5-phosphate for nucleotide synthesis, supplies nicotinamide adenine dinucleotide phosphate hydrogen (NADPH) for fat synthesis and other reductive systems, and provides a route for the metabolism of surplus pentose sugars coming from the diet. The pathway has an oxidative section converting glucose-6-phosphate into ribose-5-phosphate and it produces NADPH. The chapter explores how the nonoxidative section manipulates ribose-5-phosphate according to the needs of the cell. If a cell requires equal amounts of ribose-5-phosphate and NADPH, only the oxidative section is required.
Amino Acids, Peptides, and Proteins
This chapter discusses proteins as molecular tools. These perform an astonishing variety of functions. In addition to serving as structural materials in all living organisms, proteins are involved in diverse functions as catalysis, metabolic regulation, transport, and defence. Proteins are composed of one or more polypeptides, unbranched polymers of 20 different amino acids. The chapter looks at the genomes of organisms which specify the amino acid sequences of thousands or tens of thousands of proteins. It describes proteins as a diverse group of macromolecules that are directly related to the combinatorial possibilities of the 20 amino acid monomers. Amino acids can be theoretically linked to form protein molecules in any imaginable size or sequence.
Amphibians and Fish
This chapter begins with an analysis of the amphibian cleavage which is holoblastic and is unequal because of the presence of yolk in the vegetal hemisphere. The chapter shows how amphibian gastrulation begins with epiboly of the ectoderm followed by the invagination of the bottle cells and the coordinated involution of the mesoderm. It also reviews dorsal-ventral specification which begins with maternal messages and proteins stored in the vegetal cytoplasm. The chapter analyzes the Danio rerio, the zebrafish, which has a vertebrate model system that develops externally as a transparent embryo and completes embryogenesis in one day. It describes Kupffer's vesicle, which is a transient, fluid-filled organ in the most posterior position of the trunk.
The Ancestry of Life
This chapter details the evolutionary history of the modern groups discussed in the previous chapter and describes their ancient ancestors. The age of a group of organisms can be estimated from the age of the rocks in which the earliest fossils belonging to this group have been found. However, this is only the minimum age of the group because still earlier representatives may not have fossilized or their fossils may not have been found yet. If the rate of neutral mutation were constant over genes and lineages, DNA sequences could also be used to estimate absolute ages, independently of fossils. Ultimately, any given clade descends (to the exclusion of all other clades) from a most recent common ancestor that lived at some time in the past. The chapter considers the ancestry of Homo sapiens, Hominoidea, Primates, Eutheria, Mammalia, Amniota, Tetrapoda, Sarcopterygii, Osteichthyes (bony fishes), Gnathostomata, Chordata, Deuterostomia, Bilateria, Metazoa, Unikonta, and Eukaryota.
This chapter focuses on the process of forming new blood vessels from pre-existing ones by the growth and migration of endothelial cells — angiogenesis. It argues that this process is common during embryogenesis, although it rarely occurs in the adult. The chapter then shows why angiogenesis is essential for most tumors with respect to cancer. It explains the angiogenic switch and the mechanisms of angiogenic sprouting. Sprouting of pre-existing vessels requires major reorganization involving destabilization of the mature vessel, proliferation and migration of endothelial cells, and maturation. It is regulated by the interaction of soluble mediators and their cognate receptors. The chapter then presents the other means of tumor neovascularization and elaborates on anti-angiogenic therapy. It then looks at vascular targeting by vascular disrupting agents.
Animal identification and record-keeping
This chapter explains the identification and record-keeping of animals. It highlights the importance of keeping records such as maintaining health and welfare and aiding in conservation for captive management programmes. The chapter discusses the science behind binomial nomenclature and taxonomy. It includes a discussion on giving a temporary or permanent name to an animal such as the branding, rings, ear tags, and microchips. It looks at the degrees of intervention, invasiveness, and pain that results from these procedures. Next, the chapter shares the requirements of individual records in accordance with the Secretary of State’s Standards of Modern Zoo Practice (SSSMZP). Additionally, it notes that the International Species Information System (ISIS) has computer software formulated for zoo record-keeping.
This chapter focuses on animal welfare, which is defined as the study of an animal’s quality of life. The chapter lists environment, behaviour restrictions, and adaptation to captivity as factors affecting the welfare of zoo animals. It examines the indices used to evaluate zoo animal welfare such as life-history traits, self-directed behaviours, health, and biological processes. On the topic of meeting the needs of zoo animals, the chapter considers the concept of five freedoms, which encompasses the basic needs of captive animals ranging from malnutrition, discomfort, pain, expressing natural behaviours, and distress. The chapter highlights how legislation ensures that the best practice for animal welfare is implemented.
This chapter begins with a description of apoptosis. It defines apoptosis as a type of “cell suicide” that is intrinsic to the cell. It is an active process requiring the expression of genetically encoded proteins that every cell is capable of executing. The chapter then chronicles the molecular mechanisms of apoptosis and examines specific mutations that affect the apoptotic pathway and play a role in carcinogenesis. It also investigates how mutations in the apoptotic pathway can lead to resistance to chemotherapeutic drugs. Next, the chapter presents strategies for the design of new cancer therapeutics that target apoptosis. It also studies how caspases play a central role in apoptosis.