1055_Zoology_L3OXCIE20221-unlocked.pdf

Zoology L3 OXCIEL322/ZO1055P © Oxford Learning College 2004, 2007, 2010, 2014, 2017, 2022 We have made every effort to trace and contact all copyright holders. If notified, Oxford Learning College will be pleased to rectify any errors or omissions at the earliest opportunity Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker © 2015 Oxford Learning College. All rights reserved. Any answers to examination questions or hints to their answers were not provided by any examination board and are the sole responsibility of the authors. We are also grateful to numerous organisations for their prior permission to produce materials. A full list can be obtained by contacting Oxford Learning College during published business hours. We have made every effort to trace and contact any and all copyright holders of any materials used in this publication. At the earliest opportunity, Oxford Learning College will be pleased to rectify any and all omissions. 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Oxford Learning College works in conjunction with other institutions to bring the student the most comprehensive learning materials which aide the student in fulfilling their aims to successfully complete course mediation whether it be through an end of course examination, course work or certification through board mediation. Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker Introduction Animals have always been part of human existence – in fact we are classified as being part of the Animal Kingdom, and have been found in the oldest archaeological sites, in tombs, as symbols on ancient characters and painted on walls in caves. Zoology is the scientific study of animal life from this ancient perspective to more in-depth modern research. Its research has explained its origins as the simplest single-celled organism to the present day diverse ones containing the most complicated internal systems, not dissimilar to that found in humans. We also discuss the historic development of animals from theories of mass extinction to evolution and sustainability. Unit 1: Introduction to Zoology The first unit introduces Zoology as a subject and begins by defining animals gained the properties of life. How inorganic chemicals made the leap to organic molecules to begin the origin of life on Earth as simple celled organism is discussed. The first organisms, the prokaryote blue green algae (cyan bacteria) progress the story into a discussion on the basic building blocks of life, the cell. This brief history of the discovery of the cell as the basic unit of life, its structure and functions and the process of cellular reproduction, mitosis is included. The unit concludes with a brief look at cellular metabolism, and the importance of enzymes in a biological system, e.g. in cellular respiration and energy production and movement. Unit 2: Animal Development, evolution to individual It is clear that animals developed and became complex through the development of genetics and mixing of hereditary material. This unit examines genetics, evolution and the two basic characteristics of life, that of development and reproduction. An overview of genetic theory, from a historical perspective, followed by a closer examination of genetics at the cellular and whole animal level is given. The unit then moves logically onto evolutionary theory, setting it in a historical context pre- and post-Darwin, before discussing its implications, for animal species. The large range of strategies used by animals to ensure reproductive success is summarised, followed by a brief review of the process of development from fertilized zygote, through gastrulation to the embryo and adult individual. Unit 3: Animal Diversity: Part 1, Simple Animals This unit introduces the subject of animal diversity, beginning with a review of the various architectural patterns which occur in animal bodies. There are five major grades of organisation starting at the cellular level rising to multicellular, tissue, organ and organ-system level. The same development is reflected in the evolutionary pathways of animals and the taxonomic system currently used to classify animals supports this. The second part of the unit seeks to describe the simple animals, from unicellular protozoans through to the development of multicellular animals such as sponges and jellyfish. Various characteristics of these animals such as movement, nutrition and reproduction are briefly described. Unit 4: Animal Diversity: Part 2, Complex invertebrates Following on from the last section, this unit looks at complex invertebrates, from the simplest molluscs (including gastropods, and cephalopods), segmented worms (annelids e.g. ragworms, earthworms, leeches), to the advanced arthropods (from horseshoe crabs to crustaceans, spiders and insects), the echinoderms (starfish, sea urchins) and hemichordates (marine worms). Aspects of these groups which make them unique in the evolutionary history of the animal kingdom are discussed briefly as the group of animals is so large and varied. Species and groups of great interest to humans will therefore be covered in more detail. Unit 5: Animal Diversity: Part 3, The first vertebrates Humans most resemble this group as they share the characteristics of a backbone or “chorda” cord. The function of the vertebrae is to support, hold muscles and protect the body. This unit examines how the first vertebrate animals arose, and follows the history of animal life from the first emergence of backbone like animals, the proliferation of the fishes, through to the first walking vertebrates who moved to land, the early tetra pods and the modern amphibians. Various aspects of their life cycles, and uniqueness within the animal kingdom that cause them to evolve in the way they did e.g. move from water to land is discussed. Unit 6: Animal Diversity: Part 4, Complex vertebrates What caused animals to want to inhabit the land, and how did they adapt e.g. develop their limbs to make changes to their form in order to do this? In order for animals to be free of the need to have water in which to Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker reproduce, the evolution of non-porous eggs to the amniotic egg was necessary. This module deals with the origins of non-porous eggs, and the corresponding proliferation of reptile groups, some of which became known as 'dinosaurs'. The connections between birds and reptiles are discussed as well important features of the avian group e.g. flight, migration and navigation. Unit 7: Animal Diversity: Part 5, Mammals Mammals are small in number when compared to birds, insects and fish, however they are the most biologically differentiated e.g. from the 1.5kg bats to the blue whale. They inhabit almost every environment, even trying to conquer outer space. Mammals in all their forms are the focus of this unit. Their evolution and origin is discussed and well as the myriad of structural and functional adaptations (such as fur, highly developed nervous system and movement, and also the impact of humans on this adaptability such on domesticated pets, farm animals) the group has evolved to take advantage of the huge number of ecological niches which exist. The classification of living mammalian orders is discussed, along with specific examples of individual species. Human evolution is presented as a specific topic, although the advances in DNA modelling have helped to explain theories, full agreement on the exact path of evolution remains disputed. Unit 8: Animal activity: Part 1, Body, senses and movement Having looked at the diversity within the animal kingdom, we now focus on their life process activities, their relationship with each other and their environment. The first section discusses the various strategies animals have developed to support their body structures, e.g. internal/external skeletal systems. It then moves on to discuss how animal move through their environments, from whole animal movements to the cellular changes which enable muscle to contract. The unit concludes with a discussion on how animals have developed senses to help become aware of their environments, and how those signal are processed in the nervous system. Unit 9: Animal activity: Part 2, Maintaining the internal environment Cellular activities need to occur in a constant stable environment and how this is maintained is called homeostasis. The internal environment changes e.g. due to nutrient concentration changing or from external changes such as of temperature, need to be maintained and this involves many systems. These processes involve several systems such as osmotic regulation (water balance) temperature regulation, circulation, respiration, digestion and nutrition and finally defence against micro-organisms, i.e. immunity. This involves coordinated activities within the circulatory, nervous and endocrine systems, and the organs which act as exchange environment with the external environment such as the kidneys, lungs or gills or the skin or digestive tract. Unit 10: Animals and their environment This final unit examines how animals behave (Ethology) and deal with their external environment e.g. in social behaviour e.g. the flight patterns of a group of swallows, and communication such as the mating calls within animals. The unit continues with a discussion of animals at a global level, including the biosphere and animal distribution. We study every environment and how animals are distributed in each. Animal ecology is defined as the relation of the animal to its organic and inorganic environment, and includes an examination of predator/prey relationships and biomass pyramids. Animals have been studied at the micro- and global level throughout this course to give a brief overview of a complex and interlinked topic. Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker Unit 1: The Foundations of Animal Life CNALSL322/ZO1055C CNARDL322/ZO1055C CNARDL322/ZO1055P OXQLSL322/ZO1055C OXCIEL322/ZO1055P OXARDL322/ZO1055C OXARDL322/ZO1055P L322/D1055/1 Contents Introduction - what is zoology? Defining the properties of life The origins of life Prokaryotes, the age of cyanobacteria Cells: the building blocks of life Introduction - what is zoology? Zoology is the scientific study of animal life. Our present knowledge builds on centuries of human examination into the world of animals. Mythologies of every human culture are closely entwined with animals and the mysteries of their origin. Zoologists now examine these same mysteries using the most advanced methods and technologies available to all branches of science. Zoology can be divided into several sections, the major two being the diversity of life and understanding how animals function. This course will examine both areas, starting by describing the properties of life. It will then look at how life first began by examining how inorganic chemistry developed into organic life. Finally, the basic building block of life - the cell - is described, along with cellular metabolism. Later in the course, the activities of life including reproduction, locomotion, nutrition and sensory systems are discussed. The diversity of life is a main component of the course, and the many groups of animals are described, including how many of them conduct the activities of life. Obviously, the subject does not contain discrete separate divisions; all parts interlink with each other, and this should be kept in mind as you work through the units. At the end of each unit, there will be an assignment for you to complete and send to your tutor for marking. The last unit contains an additional essay-type assignment with multiple choices of subject. Unfortunately, in a course of this size it is not possible to provide more than a sample of the many fascinating branches of zoology, but hopefully it will whet the appetite for further study and research, whether formal or informal. © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 1 Defining the properties of life The most unique features, which separate the living system from the non-living, include chemical uniqueness, complexity and hierarchical organisation, reproduction (hereditary and variation), possession of a genetic system, metabolism, development and environmental interaction. 1. Living systems demonstrate a unique and complex molecular organisation Living systems consists of macromolecules, although they are composed of the same elements and bonds as non-living matter; their complexity makes them unique. The four major categories of biological macromolecules consist of nucleic acids, proteins, carbohydrates and lipids (fats). The general structure of these molecules evolved and stabilised early in evolutionary history. With few modifications, these molecules are identical in all life. For example, all the various proteins are made up of variations of combinations of only 20 amino acids. Other organic molecules such as lipids and carbohydrates also show great diversity, this organisation gives living systems a biochemical unity and a huge potential for diversity. 2. Living systems demonstrate a unique and complex hierarchical organisation In living systems, there is a hierarchy of organisation, in ascending order of complexity starting with macromolecules, cells, organisms, populations and species. Each level builds on the level below it and has its own internal structure and is often itself hierarchical. For example, at the individual animal level, cells are organised into tissues, e.g. haemocytes, (red blood cells) along with other blood constituents are known as the tissue, ‘blood’, and, in turn, are part of the circulatory and respiratory system. However, when examining single cell life forms it can be seen that the cellular level and the organism level are identical, in all other cases, each level is made up of units from the preceding level of organisation. 3. Living systems can reproduce themselves Life does not spontaneously arrive, but is produced from existing life via the process of reproduction. This statement does not alter the fact that life did originate from non-living material, however, this took immensely long periods of time, and conditions, which were present at the time, were very different from the current biosphere. At each level of biological hierarchy, reproduction occurs, e.g. genes replicate to produce new genes, cells replicate to produce new cells, organisms reproduce, (sexually or asexually) to produce new individuals, and populations can become fragmented and lead to new population or, in some cases, species (known as speciation). Reproduction usually involves an increase in numbers, at all levels. Reproduction at all these levels usually involves the complementary processes of variation and hereditary. Hereditary is the faithful transmission of traits from parent to offspring; variation is the production of differences between generations and individuals. This subject will be dealt with in more depth later in the course. 4. Living systems possess a genetic program For animals and other organisms, genetic material is contained within the nucleic acids, which make up DNA. DNA is a very long linear chain of subunits called nucleotides, each of which contain a sugar phosphate (dioxyribose phosphate) and one of four nitrogenous bases (adenine, cytosine, guanine and thiamine, noted as A, C, G and T). The sequence of nucleotides represents a code for the order of amino acids in the protein specified by that piece of DNA. The © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 2 correspondence between the sequence of bases in the DNA and the sequence of amino acids in the resulting protein is known as the genetic code. The same genetic code can be found in bacteria and the nuclear genome of almost all living organisms and it has thus been concluded that it arose very early in evolutionary history. 5. Living organisms maintain themselves by obtaining nutrients from their environment The essential chemical processes, which enable nutrients to become available to individual cells is know as metabolism. Metabolism includes processes such as digestion, respiration (the production of energy), and the synthesis of molecules and structures. Metabolism is often thought of as a combination of destructive (catabolic) and constructive (anabolic) reactions. In animals, many metabolic reactions occur at the cellular level, often in specific organelles found throughout the animal kingdom (details of organelles are found later in the course). The study of the performance of complex metabolic functions, and the body systems in which they take place is known as physiology, which is the subject of a large portion of this course. 6. Living organisms pass through a characteristic life cycle Development describes the characteristic changes that an organism goes through from its origin (in sexual reproduction, the fertilisation of an egg by a sperm cell) to its final adult form. It is usually exemplified by an increase in size, and often changes in shape and differentiation within the organism, from unicellular to complex higher animals. In some multi-cellular animals, very dramatic changes occur, with juvenile stages being very distinct from adult forms. The process of change between various life stages in these animals is known as metamorphosis. Among animals, the early stages of development are often fairly similar in related species. In the sections on animal diversity, stages of life histories will be examined, but due to the constraints of space, the adult stage of each example will be given priority. 7. Living organisms interact with their environment The study of how organisms interact with their environment is known as ecology. The last module in the course deals with aspects of ecology, including the geographical distribution and animal abundance. All organisms respond to stimuli in their environment; an ability called irritability. This varies from a unicellular animal moving away from a noxious substance to the complex navigational abilities of long migratory animals. The origins of life The prevailing ideas about the origins of life, up until very recently, (and are still paramount in many areas) is that life is a divine creation. The only other thoughts on the subject, adjacent to religious ones, were that life erupted repeatedly by a spontaneous eruption from non-living material. Among the existing accounts of early efforts to record these events was a recipe for, ‘making mice’, by Jean Baptise van Helmont in 1648. He recommended that, “If you press a piece of underwear soiled with sweat together with some wheat in an open jar, after about 21 days the odour changes and the ferment changes the wheat into mice”. What is most remarkable is that the mice, which came out of the underwear and wheat, were not small mice but were adult mice. Fortunately for science, in 1861, Louis Pasteur finally put, ‘spontaneous generation of life’ behind us with his famous experiment using boiled fermentable material in a flask with a long ‘S’ shaped neck. After proving no fermentation occurred when airborne organisms were prevented from © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 3 contaminating the material, he removed the neck to prove that airborne microorganisms were present. He concluded that life could not originate in the absence of previously existing life forms and proclaimed, “Never will the doctrine of spontaneous generation arise from this mortal blow”. According to the ‘big-bang’ model, the universe originated in an immense explosion 10 to 20 billion years ago. The solar system formed approximately 4.6 billion years ago from some of the material expanding out from the original explosion. In the 1920s, a Russian biochemist (Alexander Oparin) and a British biologist (J. Haldene) independently came to the conclusion that life on Earth originated after an immensely long period of ‘abiogenic evolution’. They argued that the simplest forms of life arose gradually by the progressive assembly of small molecules into more complex organic molecules that were eventually capable of self replicating, leading to the assembly of living microorganisms. Haldene and Oparin proposed that Earth’s primitive atmosphere was remarkably different to that which has existed later in Earth’s history. They theorised that it consisted of simple compounds such as water, carbon dioxide, molecular hydrogen, methane and ammonia but no oxygen. This mix was critical for understanding how life began. The organic compounds that compose living organisms are neither synthesised outside the cell, nor stable in the presence of oxygen, which is abundant in today’s atmosphere. The evidence suggests that the primitive atmosphere contained no more than a trace of oxygen, and that which was there was bound with hydrogen to form water. The ultraviolet light, which bombarded the planet, caused the formation of sugars and amino acids from the methane and ammonia in the atmosphere and early seas. Haldene believed that the early organic molecules accumulated in the primitive seas to form a ‘hot dilute soup’. In this so-called ‘primordial soup’, carbohydrates, fats, proteins and nucleic acids could have assembled to form the earliest structures capable of guiding their own replication. If the simple gaseous compounds present in the early atmosphere are mixed with methane and ammonia in a closed glass system at room temperature, chemical reactions do not occur. To produce the sort of reactions needed to form organic compounds, a continuous source of free energy is needed, sufficient to overcome the reaction activation barriers caused by the strong bonds already existing within the compounds. Ultraviolet light from the sun must have been intense during this period before the accumulation of the protective atmospheric oxygen (ozone), which is abundant in the upper atmosphere. Electrical discharges from lighting provided further energy, and thunderstorms may have been one of the most important sources of energy for organic synthesis. Volcanic energy was also probably another source of energy on the primitive Earth. One hypothesis states that life began not on the surface, but deep in the sea at the margins of hydrothermal vents. The super-heated water is thought to carry a variety of dissolved molecules from the superheated rocks, including hydrogen sulphide, methane, iron ions and sulphide ions. The many heat and sulphur tolerant bacteria naturally occurring at similar sites today back up this theory. In 1953, Miller and Urey succeeded in proving the theories of Oparin and Haldene by synthesising four organic compounds, called amino acids, when they exposed a mixture similar to that which existed on the primitive Earth to continuous electrical sparks (simulating lightening) for a week. NB. The term ‘organic’ refers broadly to compounds, which contain carbon, although many also contain varying amounts of hydrogen, oxygen, nitrogen, sulphur, phosphorus and other elements. Carbon has a great ability to bond with other carbon atoms in chains of varying lengths and configurations. Carbon bonds introduced the possibilities of an enormous variety and complexity of molecular structure. © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 4 Carbohydrates These are the most abundant organic substance and are compounds of carbon, hydrogen and oxygen, usually present in the ratio 1 carbon atom: 2 hydrogen atoms: 1 oxygen atom. Carbohydrates are used in cell protoplasm as structural elements and a source of chemical energy. Well-known forms of carbohydrate are; sugars, starches and cellulose (the woody structure in plants, which occurs in a greater quantity than all other organic material combined.) Carbohydrates are usually classified into simple sugars (monosaccharides, e.g. glucose, galactose and fructose-fruit sugar), double sugars (disaccharides, e.g. sucrose, maltose and lactose-milk sugar) and complex sugars (polysaccharides, e.g. starch - sugar store in plants, glycogen - sugar store in animals). Lipids Lipids are used as a fuel store and a building material with living organisms. They are fats and fat-like substances and are virtually insoluble in water. There are three main groups: neutral fats are the major fuel source of animals; stored fats can be derived directly from food intake, or from carbohydrates, which have, been unconverted to fat for storage. Fats are oxidised and released into the blood stream as needed to meet bodily demands. Phospholipids are important components of cell membranes, and because of their bi-polar structure can bridge two environments such as one containing water-soluble materials (such as proteins) to water insoluble materials. Steroids are complex alcohols which, although non-fats, have fat-like properties. They make up a large group of very important molecules such as cholesterol, vitamin D and the sex hormones. Amino acids and proteins Proteins are large, complex molecules composed of 20 commonly occurring amino acids: Tryptophan is a precursor of the neurotransmitter serotonin Glycine is a precursor of porphyrins such as heme Arginine is a precursor of nitric oxide Carnitine is used in lipid transport within a cell. The thyroid hormones are also amino acids. The amino acids are linked together by peptide bonds to form long polymers. The formation of peptide bonds results in the production of water. The combination of two amino acids by a peptide bond forms a dipeptide and additional amino acids can be attached at either end. The 20 different kinds of amino acids can be arranged in an enormous variety of combinations of up to several hundred amino acid units, accounting for the large variety of proteins found among living organisms. Primary protein structure A protein is not merely a long string of amino acids; the primary structure is only the first stage of the organisation of a protein. The secondary structure consists of the chains being twisted, e.g. in a helix (a twisting structure like a screw). The spirals of the chains are stabilised by hydrogen bonds between opposite amino acids in the helix. © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 5 Secondary Structure The helix can be bent and folded to give a stable 3D tertiary structure, a further level or quaternary structure is formed when more than one polypeptide chain is involved in the formation of a protein. For example haemoglobin (oxygen/carbon dioxide carrying substance in higher vertebrate blood) is composed of four polypeptide subunits held together in a single protein molecule. Structure of haemoglobin (quaternary structure) Proteins perform many functions in living organisms. They serve as the structural framework of protoplasm, and form many cellular components. Proteins also function as enzymes, the biological catalysts that mediate almost every metabolic reaction in animal systems. They function by lowering the activation energy required for specific reactions, enabling life processes to proceed at moderate temperatures. They control the reactions by which food is chemically broken down into units small enough to be absorbed by the body. They promote the synthesis of structural materials for growth and repair, plus they allow the release of energy used in respiration, growth, muscle contraction, nervous activity and many others. From molecules to living systems The fossil record shows that life existed 3.8 billion years ago, and the origin of the earliest life is thought to have occurred four billion years ago. The first living organisms were protocells; autonomous membrane-bound units with a complex functional organisation that permitted the essential characteristic of life, self-replication. The lengthy chemical evolution on the primitive earth produced several molecular components of living forms, including RNA, and this period is often referred to as the ‘RNA world’. Once this stage or organisation existed, natural selection would have begun to act, and the more rapidly replicating and successful systems were selected. Evolution of the genetic code and fully directed protein synthesis followed. The first organisms are thought to have been autotrophs (organisms which synthesise their food from inorganic sources using light or another source of energy). Organisms, which lack this ability must obtain food directly from their environments and are called heterotrophs. The earliest microorganisms are referred to as primary heterotrophs, because they relied on environmental sources for their food, and existed before any of the autotrophs. They were probably similar to members of the Clostridium genus. As the ‘chemical soup’, which existed at the time supplied all the chemical components needed, autotrophic activity was not needed. Protocells, which were able to convert inorganic material to a required nutrient, would have had a distinct advantage over the primary heterotrophs in areas where nutrients were depleted, as the number of organisms using them expanded. Evolution of autotrophic organisms most probably required the use of enzymes to catalyse the conversion of inorganic molecules to more complex ones such as carbohydrates. Autotrophs evolved by the use of photosynthesis, where hydrogen atoms obtained from water reacted with carbon dioxide obtained from the atmosphere to produce sugars and molecular oxygen. The sugars provided nutrition, but the oxygen released into the atmosphere, changed conditions on the early Earth so that life could not be generated in the same way again. When oxygen levels reached about 1% of its present level, ozone began to accumulate, and absorbed ultraviolet radiation. The accumulation of atmospheric oxygen interfered with the anaerobic cellular © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 6 metabolism of the primary heterotrophs, and oxidative (aerobic) metabolism became more competitive. Prokaryotes, the age of cyanobacteria Bacteria are known as prokaryotes, literally, ‘before the nucleus’, and contain a single large molecule of DNA, not in a membrane-bound nucleus, but in a region of the cell called the nucleoid. They have no membrane-bound organelles (see later section for discussion of cell biology) and so lack membrane-bound cell compartments such as vacuoles, endoplasmic reticulum/endoplasmic reticula, Golgi apparatus, mitochondria and chloroplasts. Cyanobacteria dominated the early oceans in the Precambrian period, and were without challenge for around two billion years, which is approximately two thirds of the history of life on our planet. The peak of their dominance occurred one billion years ago, when filamentous forms produced great floating mats on the oceans’ surface. They are still a successful group of organisms and are found in almost every conceivable habitat, from oceans to freshwater to bare rock and soil. Some have even been found to be living quite remarkably within rock. Most are found in freshwater, whilst others are marine, some occur in damp soil, or even temporarily moistened rocks in deserts. A few are endosymbionts in lichens, plants, various protists, or sponges and provide energy for the host. Some live in the fur of sloths, providing a form of camouflage. Cyanobacteria sp These bacteria are thought to be so different from other forms of life that they have been placed in a separate kingdom, Monera, although other taxonomists have proposed that there are two groups within the prokaryotes, the Eubacteria (‘true bacteria’) and Archaea or Archaebacteria, which lack muramic acid in the cell wall, which is present in all ‘true’ bacteria. Prokaryotic cell The eukaryotes have cells with membrane-bound nuclei containing chromosomes. Eukaryotes are generally larger than prokaryotes and contain a much larger amount of DNA. Cellular division is usually by some form of mitosis. Because the organisational complexity of the eukaryotes is much greater than the prokaryotes, it is difficult to understand how a linear evolutionary path led from one to another. However, the American biologist Lynn Margulis has proposed that eukaryotes did not arise from any single prokaryote, but were derived from a symbiosis of two or more types of bacteria. Mitochondria and plastids, for example, each contain their own individual complements of DNA within the cell, and have some prokaryotic characteristics. Plastids and mitochondria are closer evolutionarily to two different types of prokaryotic bacteria than to the DNA in the nucleus of the main eucalypti cell they are found in. It would be a distinct advantage for a host cell to have components, which could conduct photosynthesis (plastid with chlorophyll) and carry out oxidative metabolism. Eukaryotes may have evolved on more than one occasion. The first eukaryotes were undoubtedly unicellular, and many were photosynthetic autotrophs. Some of these lost their photosynthetic abilities and became heterotrophs, feeding on the autotrophs and the prokaryotes. As the cyanobacteria were eaten, space was made available which was exploited by other organisms. © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 7 Carnivores appeared and fed on the herbivores. A balanced ecosystem became established. By freeing space, cropping herbivores encouraged a greater variety of producers, which, in turn, promoted the evolution of more specialised croppers with carnivores at the top of a food pyramid. The explosion of evolutionary activity that followed, at the end of the Precambrian period and the beginning of the Cambrian, was unprecedented. It was thought due to the larger amount of free oxygen in the atmosphere larger multicellular organisms required the increased efficiency produced by oxidative metabolism. These metabolic pathways could not have been supported in the earlier poor oxygen conditions. Cells: the building blocks of life All living forms, (apart from viruses, and there is debate about whether these are truly ‘alive’) from unicellular amoeba to whales and giant redwoods are composed from a single type of building unit, cells. Cell theory is a unifying concept within biology. New cells arise from the division of pre-existing cells and the activities of a multicultural organism, as a whole is the sum of the activity in its constituent cells. Energy to support all of life’s activities flows from sunlight, which is captured by green plants and algae, via photosynthesis into chemical energy. Chemical energy is a form of stored energy, which can be released when it is required. The energy is used to perform electrical, mechanical and osmotic functions within the cell. Ultimately, all energy is lost through heat. This is in keeping with the second law of thermodynamics, which states that, in nature, things always proceed towards a state of entropy, or disorder. Therefore, the high degree of molecular organisation in living cells is attained and maintained only as long as energy is obtained to fuel its organisation. Even the most primitive cells are enormously complex structures. It is estimated that in a human there are over 60 trillion cells interacting in an organised partnership. In a single celled organism, all the functions of life are carried out within the one cell; in multicellular organisms, cells become specialised to perform certain functions, and may not always perform all functions, e.g. red blood cells cannot replicate themselves, as they do not have a nucleus. Studying cells Over 300 years ago, the British scientist and inventor Robert Hooke observed box like cavities in slices of cork and leaves using a primitive compound microscope, which he had developed. He called the compartments ‘little boxes or cells’. In the years that followed Hooke’s first demonstration of the powers of his microscope to the Royal society of London in 1663, biologists gradually realised that the ‘cells’ were far more important than simple containers of ‘juices’. With the exception of some eggs - the largest, in volume, cells known - cells are small and mostly invisible to the naked eye. Consequently, understanding of them parallels technological advances in the resolving power of microscopes. The Dutch microscopist A. Van Leeuwenhoek, sent descriptions of his observations of various organisms he made from 1673 to 1723. In the early 19 th century, the improved design of microscopes permitted the observation of objects only 1um in diameter. This work led to the proposal and acceptance of cell theory; that all living organisms are composed of cells. Table of measurements used in cell biology. 10–2 m cm centimetre 10–3 m mm millimetre 10–6 m um micrometre (micron) 10–9 m nm nanometre © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 8 In 1838, Mattias Schleiden announced that all plant tissue was composed of cells, followed by Theodor Schwann stating the same thing about animal cells in 1839. This statement was delayed, because animal cells are bounded only by a near invisible plasma membrane rather than the more distinctive cell wall, which characterise plant cells. In 1840, J. Purkinje introduced the term protoplasm to describe the contents of a cell. It was first thought to be a granular gel-like substance with unique life properties of its own, cells were thought of as ‘bags of thick soup containing a nucleus’. As microscopes advanced, the interior of cells became increasingly visible and, together with better staining and tissue sectioning techniques, the cells interior began to be seen as containing separate components. It is now known that a cells interior is composed of numerous cellular organelles, each of which performs a specific function. The contents of a cell are actually very highly organised and complex, in a similar way to the complexity of the organ/structural/nervous systems in an entire animal. The first electron microscopes were produced in Germany in 1931. However, light microscopes continue to be powerful tools for biological research due to portability and ease of use. One disadvantage of electron microscopes is that living tissue cannot be examined. If only fixed dead tissue is examined, it would appear that cells are static, rigid structures. The interior of a cell is in a constant state of flux, most cells are continually changing shape, pulsing, and heaving, and organelles twist and regroup constantly. These fascinating facts are gathered by time-lapse photography and sophisticated light microscopes. Components of Eukaryotic cells and their functions The table below summarises the differences between prokaryotic cells and eucharistic cells. The fundamental difference is that prokaryotes lack the membrane-bound nucleus present in all eucharistic cells. Amongst other differences are possession of membranous organelles in eukaryotes, whose structure and functions will be now be examined. Comparison of prokaryotic and eukaryotic cells Characteristic Prokaryote Eukaryote Cell size. Mostly small 1-10um. Mostly large 10-100um Genetic system. Simple circular DNA Complex DNA, bound in Nucleoid not membrane nucleus with membrane bound Cell division. Binary fission or budding Mitosis Sexual system. Absent, if present highly Present in most, male and modified female produce gametes Nutrition. Absorption/photosynthesis Absorption/ingestion/ photosynthesis Energy metabolism. No mitochondria Mitochondria present © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 9 Intracellular None Cytoplasmic streaming. Movement phagocytes, pinocytosis Flagella/cilia Not with 9+2 pattern With 9+2 microtubular pattern The cell membrane (plasma membrane, plasmalemma or ‘phospholipid bilayer’) is a semi- permeable lipid bilayer found in all cells. It contains a wide variety of biological molecules, primarily proteins and lipids, which are involved in a vast array of cellular processes, and also serves as the attachment point for both the intracellular cytoskeleton which is similar to the membranes surrounding the organelles. The cell membrane surrounds the cytoplasm of a cell and physically separates the intracellular components from the extra cellular environment, thereby serving a function similar to that of skin. The cell membrane also plays a role in anchoring the cytoskeleton to provide shape to the cell and in attaching to the extra cellular matrix to help group cells together in the formation of tissues. The fluid-mosaic model is the currently accepted concept of how membranes function. Imaging from electron microscopes show the membrane to consist of three layers, two layers of phospholipid molecules, all orientated with their water soluble ends toward the outside, and their fat-soluble portions towards the inside of the membrane. The membrane is liquid and so allows flexibility. The barrier is selectively permeable and able to regulate what enters and exits the cell, thus facilitating the transport of materials needed for survival. There are three principle ways in which substances move across the cell membrane; by diffusion (along a concentration gradient), by a mediated transport system (in which the substance binds to a specific site that assists it across the membrane) and by endocytosis (in which the substance is enclosed within a vesicle that forms on the membrane surface and detaches inside the cell). Just as material can be transported into cells by endocytosis, the plasma membrane can be extruded to release substances to the external medium (exocytosis). This process occurs in various indigestible residues brought in by endocytosis to secrete substances such as hormones or digestive enzymes. Specific proteins embedded in the cell membrane can act as molecular signals, which allow cells to communicate with each other. Protein receptors are found ubiquitously and function to receive signals from both the environment and other cells. Other proteins on the surface of the cell membrane serve as ‘markers’, which identify a cell to other cells. The interaction of these markers with their respective receptors forms the basis of cell-cell interaction in the immune system. Typical animal (eukaryotic) cell 1. Nucleolus, a ‘sub organelle’ of the nucleus. Roughly spherical-shaped, with no membrane separating it from the nucleoplasm. Nucleoli are made of protein and ribosomal DNA (rDNA). 2. Cell nucleus, the most conspicuous organelle found in a eukaryotic cell. It contains the cell's chromosomes, and is the place where almost all DNA replication and RNA synthesis occurs. The nucleus is spheroid in shape and separated from the cytoplasm by a double membrane called the nuclear membrane. The nuclear envelope isolates and protects a cell's DNA from various molecules that could accidentally damage its structure or interfere with its processing. During processing, DNA is copied (transcribed) into a special RNA, called mRNA. This mRNA is then transported out of the nucleus, where it is translated into a specific protein molecule. 3. Ribosome, a large complex cell composed of many molecules, including RNAs and proteins, and is © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 10 responsible for processing the genetic instructions carried by an mRNA. The process of converting an mRNA's genetic code into the exact sequence of amino acids that make up a protein is called translation. Protein synthesis is extremely important to all cells, and, therefore, a large number of ribosomes- sometimes hundreds or even thousands can be found throughout a cell. 4. Vesicle serves to store, transport, or digest cellular products and wastes. Lysosomes, and Golgi apparatus are both types of vesicles. 5. Rough part of the endoplasmic reticulum (ER), which is the transport network for molecules targeted for certain modifications and specific destinations, as compared to molecules that will float freely in the cytoplasm. The ER has two forms: the rough ER, which has ribosomes on its surface, and the smooth ER, which lacks them. Translation of the mRNA for those proteins that will either stay in the ER or be exported from the cell occurs at the ribosomes attached to the rough ER. 6. Golgi Apparatus (or ‘Golgi body’) is composed of a stack of membranous vesicles that function in storage, modification and packaging of protein products, especially secretary products. These vesicles do not synthesise protein, but may add complex carbohydrates to the molecules. The contents of some of these vesicles may be expelled to the outside of the cell as secretary products destined to be exported from a glandular cell. 7. Cytoskeleton, a dynamic structure that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (the movement of vesicles and organelles, for example) and cellular division. 8. Smooth endoplasmic reticulum, (also see rough endoplasmic reticulum). The smooth ER is important in lipid (fat) synthesis, detoxification and as a calcium reservoir. 9. Mitochondria are self-replicating organelles that occur in various numbers, shapes, and sizes in the cytoplasm of all eukaryotic cells. Some are rod-like, others are spherical. They may be scattered uniformly throughout the cell or may be localised near the cell surface or other regions of high metabolic activity. A mitochondrion is composed of a double membrane, the outer is smooth, and the inner is folded into a number of plate-like structures called cristae, which serve to increase surface area for metabolic reactions. Enzymes located on the cristae carry out the metabolic steps where ATP (adenosine triphosphate) is transformed to energy. Mitochondria are often known as the ‘powerhouse’ of the cell for this reason. 10. Vacuole stores food and waste. Some vacuoles store extra water. They are often described as liquid filled space and are surrounded by a membrane. 11. Cytoplasm is a homogeneous generally clear jelly-like material that fills cells. The cytoplasm consists of cytosol and the cellular organelles, except the cell nucleus. The cytosol is made up of water, salts, organic molecules and many enzymes that catalyse reactions. The cytoplasm plays an important role in a cell, serving as a ‘molecular soup’ in which the organelles are suspended and held together by a fatty membrane. 12. Lysosomes and peroxisomes are often referred to as the garbage disposal system of a cell. Both organelles are somewhat spherical, bound by a single membrane, and rich in digestive enzymes. Lysosomes can contain more than three dozen enzymes for degrading proteins, nucleic acids, and certain sugars called polysaccharides. Here we can see the importance behind compartmentalisation of the eukaryotic cell. The cell could not house such destructive enzymes if they were not contained in a membrane-bound system. 13. Centrioles are involved in cell division. Two centrioles are present in each cell. Each centriole of a pair lies at right angles to the other and is a short cylinder of microtubules, centrioles replicate before © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 11 cell division takes place. Mitosis and cell division All cells arise from the division of pre-existing cells. Cells found in most multicultural organisms originated from the division of a single cell, a zygote, which is the product of the fusion of two gametes (egg and sperm) from different individuals. Mitosis is a process of cell division, which results in the production of two daughter cells from a single parent cell. The daughter cells are identical to one another and to the original parent cell. The vast majority of cell division involves mitosis. Both growth and asexual reproduction are carried out via mitosis. The production of gametes, which involves the reduction of the number of chromosomes in each resultant gamete cell, involves a different process - meiosis - which will be discussed in the next unit. In a typical animal cell, mitosis can be divided into four principal stages, with an interstage or non-dividing stage: Prophase: at the beginning of prophase, ‘coatrooms’ (a scientific term indicating that the described has many parts), along with their centrioles replicate. The nuclear envelope disintegrates, and the two coatrooms migrate to opposite poles of the cell. At the same time, microtubules appear between the two centromeres to form a rugby ball shaped spindle, other microtubules radiate outward from each centromere to form asters. At this time, the nuclear chromatin condenses to form chromosomes visible with a light microscope. These actually consist of two identical sister chromatids, which are formed during interphase. Spindle fibres repeatedly extend and contract to ‘find’ the chromosomes within the cell. Metaphase: during a microscopic ‘tug of war’, the sister chromatids are moved to the middle of the nuclear region to form a metaphase plate. Anaphase: the centromeres divide. Sister chromatids separate and move towards the corresponding poles, pulled by the spindle fibres. Telophase: daughter chromosomes arrive at the poles and the microtubules disappear. The condensed chromatin expands (and are no longer visibly distinct chromosomes) and nuclear envelopes appear around the two daughter nuclei. During this final phase, a cleavage furrow appears on the surface of the dividing cell, and encircles it at the midline of the spindle. The cleavage furrow deepens, micro fibres of actin are present just beneath the surface of the furrow between the emerging new cells. Interaction with myosin, in a similar way to how muscle fibres contract, draws the furrow inward. Finally, the infolding edges of the plasma membrane meet and fuse, completing cell division. Interphase: the cell is engaged in metabolic activity and performing it’s prepare for mitosis (the next four phases that lead up to and include nuclear division). Chromosomes are not clearly discerned in the nucleus, although a dark spot called the nucleolus may be visible. The cell may contain a pair of centrioles (or microtubule organising centres in plants) both of which are organisational sites for microtubules. Cell mitosis Cellular metabolism All cells must obtain energy, synthesise their own internal structure, control much of their own activity and protect their boundaries from invaders. Cellular metabolism refers to the chemical processes that occur within living cells to accomplish these activities. This section will concentrate on the central metabolic processes through which matter and energy are channelled, although in a course of this size it is not possible to go into finer detail. Energy is usually expressed as the capacity to do work. It can exist in a number of different forms. © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 12 Potential energy is stored energy - energy that is currently not doing work, but has the capacity to do so. Kinetic energy is the energy of movement. Heat is the energy of temperature. Sound and light energy are also involved in some animals. Most important in animals is chemical energy, a form of potential energy, which can be converted into other states (movement, heat, sound, etc). Two laws of thermodynamics govern conversion of one type of energy to another. The first law of thermodynamics states that ‘energy cannot be created or destroyed’. That is, energy cannot be destroyed but is transformed from one form to another energy that is always conserved. The second law states that a closed system moves towards increased disorder or entropy. However, whilst the energy is contained within a living system, organisation is maintained and increased as animals develop from juvenile to adult stages (entropy is re-established, however, when the animal dies and decays). To describe the energy changes, which occur during a chemical reaction, the concept of free energy is used. This is the energy in a system that is available for doing work. In a molecule, the free energy (available energy) = energy in chemical bonds - the energy which cannot be used. The majority of reactions in cells release free energy and are therefore described as ‘exergonic’, i.e. free energy is lost. In contrast, many reactions in cells require the addition of free energy to occur. These are referred to as ‘endergonic’ and they end up with more energy than that with which they started. ATP is the ubiquitous, energy-rich intermediate chemical used by organisms to power endergonic reactions such as those required for the active transport of molecules across membranes and cellular synthesis. For any reaction to occur chemical bonds must be destabilised, some energy must be supplied to stretch and break a bond even if energy is released because of the breakage. The initial energy needed to break a bond (and start a reaction) is called the activation energy. It is a little like the energy needed to push a ball over the crest of a hill before it will spontaneously roll down the other side, with the ball liberating its potential energy as it descends. One way to activate chemical reactants is to heat them. This causes an increase in the rate of molecular collisions enabling bonds to be broken and the reaction to take place. Metabolic reactions must occur at within a narrow temperature/range, which is usually too low for reactions to proceed. Instead, living systems have evolved catalysts as an alternative method. Enzymes Enzymes are the catalysts of the living world, and are complex molecules that vary in size from small simple proteins to large highly complex molecules. Many enzymes are pure proteins. Others have small non-protein groups called ‘cofactors’. In many cases, these are metallic ions but may also be organic. These co-enzymes are derived from vitamins supplied via diet. An enzyme functions by associating in a highly specific way with its substrate, the molecule whose reaction it catalyses. Enzymes have an active site which correspond directly to the substrate and binds to it. Enzyme/substrate active site The resulting enzyme-substrate complex provides pressure that stretches the particular bonds and the ES complex soon disassociates into products and enzyme. Enzymes are highly specific, and different enzymes are required for every step of a metabolic pathway, each enzyme can catalyse only one reaction. Adenosine 5'-triphosphate (ATP) is a multifunctional nucleotide that is most important as a ‘molecular currency’ of intracellular energy transfer. In this role, ATP transports chemical energy © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 13 within cells for metabolism. It has very high- energy bonds, which are quite unstable, thus the energy of ATP is readily released when ATP is converted to ADP. ATP is not a store of energy rather it is produced by one set of reactions and is almost immediately used by another. It is formed, as it is needed, primarily by oxidative processes in the mitochondria. Cellular respiration Cellular respiration describes the metabolic reactions and processes that take place in a cell or across the cell membrane to obtain biochemical energy from fuel molecules and the release of the cells' waste products. Energy is released by the oxidation of fuel molecules and is stored as ‘high-energy’ carriers. Fuel molecules, commonly used by cells in respiration, include glucose, amino acids and fatty acids, and a common oxidising agent (electron acceptor) is molecular oxygen (O2). There are organisms, however, that can respire using other organic molecules as electron acceptors instead of oxygen. Organisms that use oxygen as a final electron acceptor in respiration are described as aerobic, while those that do not are referred to as anaerobic. Aerobic respiration requires oxygen in order to generate energy (ATP). It is the preferred method of pyruvate breakdown from glycolysis and requires that pyruvate enter the mitochondrion to be fully oxidised. The product of this process is energy in the form of ATP. Simplified Reaction: C6H12O6 (aq) + 6O2 (g) → 6CO2 (g) + 6H2O (l) ΔHc -2880 kJ Between 36-38 ATP molecules can be made per oxidised glucose molecule during cellular respiration. Generally, 38 ATP molecules are formed from aerobic respiration. However, this maximum yield is never quite reached due to losses (leaky membranes) as well as the cost of moving pyruvate and ADP into the mitochondrial matrix. Aerobic metabolism is 19 times more efficient than anaerobic metabolism (which yields 2 mol ATP per 1 mol glucose). They share the initial pathway of glycolysis, but aerobic metabolism continues with the Krebs cycle and oxidative phosphorylation. The post glycolytic reactions take place in the mitochondria in eukaryotic cells, and in the cytoplasm in prokaryotic cells. ATP is produced at various points through cellular metabolism, in various other complex metabolic pathways such as glycolysis and the Krebs cycle. Both are beyond the scope of this unit. Management of metabolism The complex pattern of enzymatic reactions, which constitute metabolism, cannot be explained entirely in terms of physic-chemical laws or chance happenings. Although some enzymes do indeed ‘go with the flow’, the activity of others is strictly controlled. For example, if in the former case the function of an enzyme is to convert A to B, if B is removed by conversion to another compound, the enzyme will tend to restore the original ration of B to A. Since many enzymes also function in reverse, if A is removed, excess B will be converted back into A. This automatic compensation (equilibrium) is not sufficient to explain all that takes place in an organism’s metabolic pathway. Mechanisms exist for regulating enzymes, both in quantity and activity. In bacteria, genes leading to synthesis of an enzyme are switched on or off, depending on the presence or absence of a substrate molecule. In this way, the quantity of an enzyme is controlled, albeit by a relatively slow process. Other mechanisms exist that alter the structure of an enzyme making it unable to bind to its substrate, for example the presence of (or a particular concentration of) another chemical can deform an enzyme, rendering it temporarily ineffective. As well as being mechanically changed, most © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 14 enzymes exist in an active and inactive form, which may be chemically different. This unit has discussed how life began and is maintained on a cellular level. The next unit will discuss how life is reproduced and maintained through reproduction at the cellular, animal and population levels. © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 15 References http://www.naturalhistorymag.com/topics/evolution http://upload.wikimedia.org/wikipedia/commons/5/53/Protein_Composite.jpg http://www.scientificpsychic.com/fitness/glycogen.gif http://www.brooklyn.cuny.edu/bc/ahp/SDPS/SD.PS.proteins.html http://www.ucmp.berkeley.edu/bacteria/cyanointro.html http://www.terrebonneonline.com/bacteria2.jpg http://www.daviddarling.info/images/cell_structure.jpg http://en.wikipedia.org/wiki/Mitosis Further Reading Alberts, B., Bray, D., Hopkin, K., Johnson, A., Roberts, K., Lewis, J., Raff, M., and Walter, P. (2013), Essential Cell Biology, 4th edn., Garland Science Allaby, M., (2014), A Dictionary of Zoology 4th edn., OUP Oxford Madigan, M., Martinko, J., Addison, Bender, K., Buckley, D., and Stahl, (2014), Brock Biology of Microorganisms, 14th edn., Pearson © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 16 Unit 2: Animal Development, from Evolution to Individual CNALSL322/ZO1055C CNARDL322/ZO1055C CNARDL322/ZO1055P OXQLSL322/ZO1055C OXCIEL322/ZO1055P OXARDL322/ZO1055C OXARDL322/ZO1055P L322/D1055/2 Contents Genetics Mendel and hereditary Meiosis, gamete production Evolution Pre-Darwin theory Darwin’s evidence Microevolution (change with species) Macroevolution (mass extinctions) The reproductive process Asexual reproduction Sexual reproduction Principles of development Fertilisation Cleavage and early development Gastrulation Development of systems and organs © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 17 Genetics A basic principle of modern evolutionary theory is that organisms attain their diversity through hereditary modifications of pre-existing similar ancestors. All known animals are related by descent from common ancestors. Hereditary establishes the continuity of life, although offspring usually vary in subtle ways from their parents. Some characteristics show resemblances to one or other parent, others are a blend of the two. What is actually inherited by an offspring are ‘genes’ (the genotype) which, under environmental factors, guide the physical characteristics, which are seen (the phenotype). The gene is the unit of inheritance, the basis for every characteristic that appears in an organism. The study of what genes are and how they work is called genetics. It is a science that deals with the underlying causes of resemblance and variation between individuals, populations and species. Genetics is one of the most important and unifying concepts in biology. It has shown that all living forms use the same information storage, transfer and translation system, and it provides an explanation for both the stability of all life and its descent from a common ancestral from. Some of the terms used in genetics can seem a little complex. However, if you work your way through slowly the connections will become clear. It is not necessary to fully understand all of the genetic theory, but the basic principles are very important. Mendel and inheritance Mendelian inheritance is a set of primary tenets relating to the transmission of characteristics from parent organisms to their offspring. They were derived from the work of the Austrian Monk, Gregor Mendel, and published in 1865 and 1866 but were ‘re-discovered’ in 1900. When his ideas were integrated with the chromosome theory of inheritance, by Thomas Hunt Morgan, in 1915, they became the core of classical genetics. Mendel’s now classic observations were based on garden peas, because pure strains (offspring always identical to parent plants) had been produced over a long period of time by careful selection in the Abbey gardens. He chose to use single characteristics (traits), which displayed sharp contrasts between different conditions - e.g. short or tall plants, yellow or green peas, smooth or wrinkled peas. He crossed one plant with one characteristic (e.g. green peas) with the other (yellow peas) by artificial fertilisation. When the cross-fertilised plant bore seeds he noted the characteristics of the hybrids grown from these seeds (know as the F1 generation). The ‘re-discovery’ made Mendelism an important but controversial theory. Its most vigorous promoter in Europe was William Bateson, who coined the term ‘genetics’, ‘gene’, and ‘allele’ to describe many of its tenets. The model of heredity was highly contested by other biologists, because it implied that heredity was discontinuous, in opposition to the apparently continuous variation observed in the natural world - e.g. people are not only short or tall, but may be almost a continuous scale of height. Many biologists dismissed the theory, because they were not sure it would apply to all species, as there seemed to be very few ‘true Mendelian characters’ in nature. However, later work by biologists and statisticians showed that if multiple Mendelian factors were involved for individual traits, they could produce the diverse amount of results observed in nature. © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 18 The Law of Segregation, also known as Mendel's First Law, states that, ‘in the formation of gametes, paired factors specifying different phenotypes (visible traits) segregate independently from each other’. (See section on meiosis later in the module). There are four underpinning facts, which support this theory. 1. Alternative versions of genes account for variations in inherited characteristics. This is the concept of alleles. Alleles are different versions of a gene that impart the same characteristic. For example, each human has a gene that controls eye colour, but there are variations among these genes in accordance with the specific colour for which the gene ‘codes’, e.g. blue, brown, green, etc. The locus of a gene is the area of a chromosome where a particular gene is found (where on a chromosome the gene is), e.g. at the locus of the agouti (tabby) gene in the cat, either the agouti (A) or non-agouti (a) allele can be found. 2. For each characteristic, an organism (if sexual reproduction occurs) inherits two alleles, one from each parent. This means that when somatic (non-gamete) cells are produced (they have pairs of chromosomes), one allele comes from the mother and one from the father. These alleles may be identical (true-breeding organisms or homozygous), or different (hybrids or heterozygous). The allele of a gene represents the different forms that genes can take. 3. Alleles of a gene exhibit dominance. If the two alleles differ, then one, the allele that encodes the dominant trait, is fully expressed in the organism's appearance; the other, the allele encoding the recessive trait, has no noticeable effect on the organism's appearance. In other words, only the dominant trait is seen in the phenotype of the organism. This allows recessive traits to be passed on to offspring even if they are not expressed. An allele is said to be dominant when its expression prevails over any other copy of the gene in the cell. For example, agouti (tabby) is a dominant allele in the cat, so any cat having at least one agouti allele will have a visibly tabby coat. When expressing genetic information, a particular shorthand is used; all dominant alleles are referred to with a capital letter, e.g. A, B, C. Recessive alleles need to be present on both chromosomes to be expressed, i.e. no dominant allele can be present for the recessive characteristic to be ‘seen’. If a recessive allele is paired with a dominant allele, it will not be ‘visible’ in the organism. For example, a cat that has inherited the agouti gene from both parents will be AA and tabby in appearance (genotypically and phenotypically tabby). The cat that inherits one agouti and one non-agouti gene will be Aa, and will appear to be tabby in appearance (heterozygous genotype, tabby phenotype). Only if the cat inherits non-agouti from both parents, will the cat have a solid coloured coat aa (homozygous recessive genetically, phenotype non tabby). 4. The two alleles for each characteristic segregate during gamete production. This means that each gamete will contain only one allele for each gene. This allows the maternal and paternal alleles to be combined in the offspring, ensuring variation. A tool often used by animal breeders is the Punnet square. It can be used to determine the potential different genotypes of offspring from a specific mating. The alleles contained in the gametes from one parent are placed along the top, those from the other along the side. Since each gamete contains only one of a pair, only a single letter for each gene is present. For example, continuing with the example of agouti and non-agouti (tabby and self pattern), if both parents are heterozygous for tabby, the following © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 19 Punnet square would result. Example 1: both parents heterozygous 50% eggs carrying A 50% eggs carrying a 50% sperm carrying A 25% AA homo tabby 25% Aa hetero tabby 50% sperm carrying a 25% Aa hetero tabby 25% aa homo self Each sperm cell carries either A (agouti) or a (non-agouti), each egg cell will similarly carry either an A or a. The four inner sections represent the possible genotypes of the offspring. A quarter will be AA homozygous tabby, a quarter homozygous self aa, and 50% will be heterozygous tabby Aa. As A is dominant to a, all the kittens will be phenotypically tabby. Mathematically, the visible traits seen in kittens will be three tabbies, and one self. NB. However, as each potential kitten is formed of a random pairing of gametes, and the number of kittens present in a litter is variable, the actual ratio found in a particular litter may not be as above, it is also possible that all the kittens will be tabby, or 50% non-tabby. This type of square is also useful if the parents genotype is unknown, it can be useful to determine whether a parent is homozygous or heterozygous for a characteristic, This is known as a test mating - i.e. mating a heterozygous ‘suspect’ parent (is it AA or aa?) to a homozygous recessive cat e.g. aa. Then, if any of the offspring were non-tabby, the suspect parent must be heterozygous. Example 2: determining parent genotype Homozygous recessive a Homozygous recessive a Tabby A or a Aa or aa Aa or aa Tabby A or a Aa or aa Aa or aa Any aa offspring means the parent is a heterozygote for the gene in question. Again, such a test mating would have to be repeated several times to determine if the parent was a heterozygote. For example, you could flip a coin five times and gets heads every time, but assuming the coin had two heads, (and no tails) there would not be a valid conclusion unless a great many more ‘flips’ had been carried out. Even though statistics say heads and tails should occur in equal numbers, this does not always occur in a limited sample. Mendel’s Second Law: The Law of Independent Assortment, states that the inheritance pattern of one trait will not affect the inheritance pattern of another. In terms of gene theory, this means that genes located on different pairs of homologous chromosomes assort independently during meiosis. While his experiments with mixing one trait always resulted in a 3:1 ratio (example 1) between dominant and recessive phenotypes, his experiments with mixing two traits (dihybrid cross) showed 9:3:3:1 ratios. Example 2 shows that each of the two genes are independently inherited with a 3:1 ratio. Mendel concluded that different traits are inherited independently of each other. © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 20 Example 2: dihybrid cross In the pea plant, two characteristics for the peas, shape and colour, can be used to as an example of a dihybrid cross in a Punnett square. R is the dominant gene for roundness of shape in pea seeds, with r denoting the recessive wrinkled shape. Y = dominant yellow pea, and y = recessive green coloured pea. The gametes for the Punnett square from the parent plants are, therefore, RY (round and yellow), Ry (Round and green), rY, (wrinkled and yellow) and ry (wrinkled and green). RY Ry rY ry R RRYY RRYy RrYY RrYy Y R RRYy RRyy RrYy Rryy y r RrYY RrYy rrYY rrYy Y r RrYy Rryy rrYy rryy y The result in this cross is a 9:3:3:1 phenotypic ratio, as shown by the colours, where yellow represents a round yellow (both dominant genes) phenotype, green representing a round green phenotype, red representing a wrinkled yellow phenotype, and blue representing a wrinkled green phenotype (both recessive genes). The reason for this is that during meiosis (gamete producing cell division), the member of any pair of homologous chromosomes (received by a particular gamete) is independent of which member of any other pair of chromosomes it receives. Multiple alleles Whereas an individual can have no more than two alleles at a particular locus (one on each chromosome of a pair), many more dissimilar alleles can exist in a population. Multiple alleles arise through mutations at the same gene locus over time. Any gene may mutate, and can give rise to slightly different alleles at the same locus, however unless the more recessive forms occur in a homozygous animal, they may never be actually seen phenotypically. For example, unless two albino rabbits (or those carrying the recessive albino gene) mate, no albinos will be seen, even though the gene will be passed through successive generations. Gene interaction The types of crosses presented above are simple in that the trait variation results from the action of a single gene. In reality, many traits are the result of interaction between two or more genes, and many different genes affect individual characteristics (polygenetic inheritance). © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 21 In addition, many genes have more than a single effect on a phenotype, this is known as pleiotrophy, e.g. a gene which influences eye colour, may also mask or prevent the expression of an allele on another locus acting on the same trait. This is known as epistasis. Another form of interaction occurs when several different alleles produce a cumulative effect on the same characteristic. The number of chromosomes in any organism is relatively small, compared with the huge number of traits, so therefore, each chromosome contains many genes. All genes on the same chromosome are said to be linked. Crossing over Linkage is, however, seldom complete. When performing crosses with animals such as Drosophila (fruit fly), linkage traits separate in a small percentage of offspring. These separations of alleles on the same chromosomes are due to crossing over. During the first phase of gamete producing cell division, (meiosis) paired homologous chromosomes break and exchange equivalent portions, thus genes can ‘cross over’ from one chromosome to its homologous partner. Meiosis and gamete production Meiosis is the process by which one diploid (each chromosome has an alternate within the cell) eukaryotic cell divides to generate four haploid (has non-paired chromosomes) cells called gametes. The genetic material is replicated once and separated twice, producing four haploid cells each containing half of the original cell's chromosomes. These resultant haploid cells can fuse with other haploid cells of the opposite sex during fertilisation to create a new diploid cell or zygote. The word ‘meiosis’ comes from the Greek meioun, meaning ‘to make smaller’, as it results in a reduction in chromosome number in the gamete cell. Meiosis is essential for sexual reproduction and occurs in all eukaryotes that reproduce sexually. Without the halving of the number of chromosomes, fertilisation would result in zygotes that have twice the number of chromosomes than the zygotes of the previous generation. As chromosomes of each parent undergo genetic recombination during meiosis, each gamete, and thus each zygote, will be unique genetically. Thus meiosis and sexual reproduction produce genetic variations. © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 22 Meiosis uses many of the same biochemical and physical mechanisms employed during mitosis to accomplish the redistribution of chromosomes. There are several features unique to meiosis, most importantly the pairing and genetic recombination between homologous chromosomes. Recombination and independent assortment allow for a greater diversity of genotypes in the population, allowing a species to maintain stability and adapt to environmental changes. Evolution Pre-Darwin theory Before the 18th century, speculation on the origin of species rested on creationism, where the world has remained constant since the Earth was created by divine being (s) depending on the religion. Early Greek philosophers (Xenophanes, Empedocles and Aristotle) developed a theory that species change, as they recognised fossils as evidence that some organisms existed in the past that were not present in their time. However, they assumed these organisms died from natural disasters. Lamarckism French biologist Jean Baptiste de Lamark proposed the first complete explanation of evolution (called the inheritance of acquired characteristics) in 1809, the year Charles Darwin was born. Lamark proposed his mechanism to account for extinctions over time, using fossil evidence that certain animals no longer existed. He proposed that organisms striving to meet the demands of their environment acquire adaptations, which they then pass on to their offspring, e.g. an ancestral giraffe had to stretch neck and legs to reach high food items as lower down food was unavailable, resulting in longer limbs/necks, which are then inherited by their young. This transformational concept of evolution proposed that individual organisms transform their characteristics to produce overall species changes (evolution). Darwin’s theory is a contrasting variational theory, caused by distribution of genetic variation in populations and differential survival/reproduction in individuals with different hereditary traits. Uniformitarianism The geologist Charles Lyell proposed (in 1830) that the laws of chemistry and physics remain the same throughout the history of the Earth, and that past geological events occurred by natural processes acting over long periods, explaining the formation of fossil bearing rocks. Lyell also stressed the gradual nature of geological changes over very long periods, an idea which greatly influenced Darwin. Charles Darwin Darwin developed his interest in natural history while studying first medicine, then theology. His five-year voyage on the Beagle established him as a geologist whose observations and theories supported Lyell's uniformitarian theories. Puzzled by the geographical distribution of wildlife and fossils he collected on the voyage, Darwin investigated the transmutation of species (the gradual change of one species into another) and conceived his theory of natural selection in 1838. His 1859 book, On the Origin of Species, established evolution by common descent as the dominant scientific explanation of diversification in nature. Darwinian evolutionary theory: the evidence Perpetual change The main underpinning idea behind Darwinian evolution is that the living world is neither constant, nor in © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 23 a state of perpetual cycling, but is nevertheless constantly changing. Evidence for this perpetual change is seen directly in the fossil record. A fossil is a remnant of past life uncovered from the crust of the earth. They come in various forms from complete remains (e.g. mammoths, or insects in amber) to actual hard parts (teeth and bones), petrified skeletal parts that are infiltrated with silica or other minerals (ostraderms and molluscs) and finally other fossils including, moulds, casts, impressions and coprolites (fossil excrement). Because many organisms left no fossils, a complete record of the past is probably never going to be available. However, discovery of new fossils and reinterpretation of previous discoveries expand our knowledge of how animal life has changed over time. Fossil insect in amber Carcharodontosarus Coprolite and Megaladon teeth The fossil record is, however, biased because preservation is selective with vertebrate skeletal parts and invertebrate shells/other hard body parts leaving superior records. Soft-bodied animals such as worms and jellyfish are seldom fossilised. Fossils are deposited in stratified layers, with new deposits on top of older ones, thus a sequence occurs with the ages of fossils being directly related to their depth within stratified layers, and different layers are characterised by the fossils they contain. Unfortunately, layers are rarely undisturbed, geological processes such as erosion or human intervention result in incomplete disturbed evidence, which is difficult to interpret. Evolutionary trends The fossil record allows evolutionary changes to be seen over very long periods of time. Species arise and become extinct repeatedly throughout the history of the Earth. Animal species typically survive approximately one million to ten million years, although their duration is highly variable. Trends (directional changes in the characteristic features or patterns of diversity in a group of organisms) can often be seen in particular groups of species. One of the better-documented cases is the fossil evidence of the evolution of horses from the Eocene era to the present. Other species replaced many different species throughout time (only the main groups are depicted below). The three characteristics, which show the clearest trends in horse evolution are body size, foot structure and tooth structure. Compared to modern horses, extinct genera were small, with teeth having a small grinding surface, and feet with a larger number of toes (four). Throughout the Oligocene, Miocene, Pliocene and Pleistocene eras, there were continuing patterns of new genera arising as the older ones became extinct. In each case, a net increase in body size, grinding surfaces of teeth and a reduction in the number of toes occurred. As the number of toes decreased, the central digit became increasingly prominent, until only this digit remained. The fossil record shows a net change not only in the characteristics of horses, but also variation in the numbers of different horse genera and numbers of species that have existed through time. The sole survivor of this largely extinct group is the genus equus. © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 24 Common ancestry Darwin proposed that all living things have descended from a common ancestral organism. Life’s history is often depicted as a branching tree, called a phylogeny. Pre-Darwinian evolutionists, including Lamark, advocated multiple independent origins to life, each of which gave rise to lineages, which changed throughout time without extensive branching. The classification and phylogeny of animal species is examined in the next module. Homology Darwin recognised the major source of evidence for common ancestry was the idea of homology. Anatomical structures that perform the same function in different biological species and evolved from the same structure in an ancestral species are called homologous. A classic example of homology is the limb skeleton of vertebrates. Bones of vertebrate limbs maintain characteristic structures and patterns of connection despite diverse modification for different functions. The pentadactyl limb Ontogeny, phylogeny and recapitulation Ontogeny is the history of the development of an organism throughout its entire life. Early developmental land embryological features contribute greatly to our knowledge of homology and common decent. The German zoologist Ernst Haeckel (a contemporary of Darwin) believed that each successive stage in the development of an individual represented one of the adult forms that appeared in its evolutionary history. The human embryo, having gill depressions, was believed to resemble the adult appearance of a fish-like ancestor. Thus, ontogeny (individual development) recapitulates (repeats) phylogeny (evolutionary decent). This is also known as recapitulation or the biogenetic law, although later theorists proposed that early developmental features were simply more widely shared amongst different animal © OXL/CN/AN 2022 Student No: PD24-51917-ZOCIE15 Email: [email protected] Name: Grace Walker 25 groups than latter ones. The adult stages of animals with relatively simple ontogenies simply resemble the early stages in the development of more complex organisms. Ontogeny in chordates Multiplication of species Multiplication of species over time is the logical result of Darwin’s theory of common descent. A branch point on the evolutionary tree occurs when an ancestral species splits into two different ones. Members of a species are descended from a common ancestor, are reproductively compatible, and have consistency of genotype/phenotype. Speciation is the process by which a single population of organisms becomes reproductively unique and a separate species. Biological barriers, which prevent different species reproducing, are called reproductive barriers. Speciation is thought to occur in two ways: Speciation that results from the evolution of reproductive barriers between populations that are geographically separated is called allopatric speciation. It can begin in two ways, firstly by vicariant speciation, where geological changes fragment a species habitat. In this instance, say a flood or fault divides a habitat, more than one species is usually affected at a time. Alternatively, allopathic speciation can be due to a founder event, when a small number of individuals disperse to a distant area where no members of their species currently

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