12.2: Introduction - Biology

12.2: Introduction - Biology

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The pH of an environment can affect the growth and survival of the microbes in that environment. pH is a measure of the hydrogen ion concentration or activity, in a solution, expressed as:

[-log_{10}[H+] onumber ]

Every organism has an optimal pH range at which it will grow. If the pH is too high or too low it can affect things like the solubility of molecules, denaturation of proteins/enzymes, membrane transport, proton-motive force/membrane potential, etc. These changes can be devastating to a bacterial population. We have exploited this in the production of foods, for example, pickling is a common method of food preservation and compounds like citric acid are often added to food products to lower the pH and prevent spoilage or toxin formation.

Most bacteria are neutrophils while fungi prefer a more acidic environment from pH 4-6. Archaea are found in all ranges. Nonetheless, all microbes keep their internal environment near neutral and some have developed mechanisms to allow them to survive in the more extreme ranges.

In microbiology we also use a variety of biochemical tests based on pH changes in the media as diagnostic tests. Many bacteria produce acids that are released into the environment as metabolic products of fermentation. These acids can have a big effect on the pH of a closed system like a test tube or agar plate. You will utilize some of these biochemical tests in the future to help you identify bacteria and key characteristics of them.

The pH scale is a tool to measure the relative acidity of solutions, food, natural environments like lakes (water), and as stated, biochemical reactions. The scale is logarithmic reflecting the definition of pH and actually making the scale easy to use. pH 0, which is the most acidic level, has a hydrogen ion concentration of 100 moles/L; pH 14, the most alkaline, has a hydrogen ion concentration of 10-14 moles/L. Pure water is neutral and therefore has a pH of 7 (10-7 moles/L). Each pH level represents then a tenfold decrease or increase in hydrogen ion concentration. So, pH6 is ten times more acidic than pH 7, and ten times more alkaline than pH 5.

There are 3 main groups of microbes classified by the pH range they can survive in:

Acidophiles: pH 0-5.5

Neutrophiles: pH 5.5-8.0

Alkaliphiles: pH 8.0-11.5


Genetics is the study of heredity. Johann Gregor Mendel set the framework for genetics long before chromosomes or genes had been identified, at a time when meiosis was not well understood. Mendel selected a simple biological system and conducted methodical, quantitative analyses using large sample sizes. Because of Mendel’s work, the fundamental principles of heredity were revealed. We now know that genes, carried on chromosomes, are the basic functional units of heredity with the capability to be replicated, expressed, or mutated. Today, the postulates put forth by Mendel form the basis of classical, or Mendelian, genetics. Not all genes are transmitted from parents to offspring according to Mendelian genetics, but Mendel’s experiments serve as an excellent starting point for thinking about inheritance.

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    External and Chemical Barriers

    The body has significant physical barriers to potential pathogens. The skin contains the protein keratin, which resists physical entry into cells. Other body surfaces, particularly those associated with body openings, are protected by the mucous membranes. The sticky mucus provides a physical trap for pathogens, preventing their movement deeper into the body. The openings of the body, such as the nose and ears, are protected by hairs that catch pathogens, and the mucous membranes of the upper respiratory tract have cilia that constantly move pathogens trapped in the mucus coat up to the mouth.

    The skin and mucous membranes also create a chemical environment that is hostile to many microorganisms. The surface of the skin is acidic, which prevents bacterial growth. Saliva, mucus, and the tears of the eye contain an enzyme that breaks down bacterial cell walls. The stomach secretions create a highly acidic environment, which kills many pathogens entering the digestive system.

    Finally, the surface of the body and the lower digestive system have a community of microorganisms such as bacteria, archaea, and fungi that coexist without harming the body. There is evidence that these organisms are highly beneficial to their host, combating disease-causing organisms and outcompeting them for nutritional resources provided by the host body. Despite these defenses, pathogens may enter the body through skin abrasions or punctures, or by collecting on mucosal surfaces in large numbers that overcome the protections of mucus or cilia.

    Table of Contents


    1.1 Introduction 1

    1.2 Basic Definitions and Notation 2

    1.3 First-Order Equations 6

    1.4 Second-Order and Higher-Order Equations 8

    1.5 First-Order Linear Systems 14

    1.6 An Example: Leslie&rsquos Age-Structured Model 18

    1.7 Properties of the Leslie Matrix 20

    1.8 Exercises for Chapter 1 28

    1.9 References for Chapter 1 33

    1.10 Appendix for Chapter 1 34

    1.10.1 Maple Program:Turtle Model 34

    1.10.2 MATLAB® Program:Turtle Model 34


    2.1 Introduction 36

    2.2 Basic Definitions and Notation 37

    2.3 Local Stability in First-Order Equations 40

    2.4 Cobwebbing Method for First-Order Equations 45

    2.5 Global Stability in First-Order Equations 46

    2.6 The Approximate Logistic Equation 52

    2.7 Bifurcation Theory 55

    2.7.1 Types of Bifurcations 56

    2.7.2 Liapunov Exponents 60

    2.8 Stability in First-Order Systems 62

    2.9 Jury Conditions 67

    2.10 An Example: Epidemic Model 69

    2.11 Delay Difference Equations 73

    2.12 Exercises for Chapter 2 76

    2.13 References for Chapter 2 82

    2.14 Appendix for Chapter 2 84

    2.14.1 Proof of Theorem 2.1 84

    2.14.2 A Definition of Chaos 86

    2.14.3 Jury Conditions (Schur-Cohn Criteria) 86

    2.14.4 Liapunov Exponents for Systems of Difference Equations 87

    2.14.5 MATLAB Program: SIR Epidemic Model 88


    3.1 Introduction 89

    3.2 Population Models 90

    3.3 Nicholson-Bailey Model 92

    3.4 Other Host-Parasitoid Models 96

    3.5 Host-Parasite Model 98

    3.6 Predator-Prey Model 99

    3.7 Population Genetics Models 103

    3.8 Nonlinear Structured Models 110

    3.8.1 Density-Dependent Leslie Matrix Models 110

    3.8.2 Structured Model for Flour Beetle Populations 116

    3.8.3 Structured Model for the Northern Spotted Owl 118

    3.8.4 Two-Sex Model 121

    3.9 Measles Model with Vaccination 123

    3.10 Exercises for Chapter 3 127

    3.11 References for Chapter 3 134

    3.12 Appendix for Chapter 3 138

    3.12.1 Maple Program: Nicholson-Bailey Model 138

    3.12.2 Whooping Crane Data 138

    3.12.3 Waterfowl Data 139


    4.1 Introduction 141

    4.2 Basic Definitions and Notation 142

    4.3 First-Order Linear Differential Equations 144

    4.4 Higher-Order Linear Differential Equations 145

    4.4.1 Constant Coefficients 146

    4.5 Routh-Hurwitz Criteria 150

    4.6 Converting Higher-Order Equations to First-OrderSystems 152

    4.7 First-Order Linear Systems 154

    4.7.1 Constant Coefficients 155

    4.8 Phase-Plane Analysis 157

    4.9 Gershgorin&rsquos Theorem 162

    4.10 An Example: Pharmacokinetics Model 163

    4.11 Discrete and Continuous Time Delays 165

    4.12 Exercises for Chapter 4 169

    4.13 References for Chapter 4 172

    4.14 Appendix for Chapter 4 173

    4.14.1 Exponential of a Matrix 173

    4.14.2 Maple Program: Pharmacokinetics Model 175


    5.1 Introduction 176

    5.2 Basic Definitions and Notation 177

    5.3 Local Stability in First-Order Equations 180

    5.3.1 Application to Population Growth Models 181

    5.4 Phase Line Diagrams 184

    5.5 Local Stability in First-Order Systems 186

    5.6 Phase Plane Analysis 191

    5.7 Periodic Solutions 194

    5.7.1 Poincaré-Bendixson Theorem 194

    5.7.2 Bendixson&rsquos and Dulac&rsquos Criteria 197

    5.8 Bifurcations 199

    5.8.1 First-Order Equations 200

    5.8.2 Hopf Bifurcation Theorem 201

    5.9 Delay Logistic Equation 204

    5.10 Stability Using Qualitative Matrix Stability 211

    5.11 Global Stability and Liapunov Functions 216

    5.12 Persistence and Extinction Theory 221

    5.13 Exercises for Chapter 5 224

    5.14 References for Chapter 5 232

    5.15 Appendix for Chapter 5 234

    5.15.1 Subcritical and Supercritical Hopf Bifurcations 234

    5.15.2 Strong Delay Kernel 235


    6.1 Introduction 237

    6.2 Harvesting a Single Population 238

    6.3 Predator-Prey Models 240

    6.4 Competition Models 248

    6.4.1 Two Species 248

    6.4.2 Three Species 250

    6.5 Spruce Budworm Model 254

    6.6 Metapopulation and Patch Models 260

    6.7 Chemostat Model 263

    6.7.1 Michaelis-Menten Kinetics 263

    6.7.2 Bacterial Growth in a Chemostat 266

    6.8 Epidemic Models 271

    6.8.1 SI, SIS, and SIR Epidemic Models 271

    6.8.2 Cellular Dynamics of HIV 276

    6.9 Excitable Systems 279

    6.9.1 Van der Pol Equation 279

    6.9.2 Hodgkin-Huxley and FitzHugh-Nagumo Models 280

    6.10 Exercises for Chapter 6 283

    6.11 References for Chapter 6 292

    6.12 Appendix for Chapter 6 296

    6.12.1 Lynx and Fox Data 296

    6.12.2 Extinction in Metapopulation Models 296


    7.1 Introduction 299

    7.2 Continuous Age-Structured Model 300

    7.2.1 Method of Characteristics 302

    7.2.2 Analysis of the Continuous Age-Structured Model 306

    7.3 Reaction-Diffusion Equations 309

    7.4 Equilibrium and Traveling Wave Solutions 316

    7.5 Critical Patch Size 319

    7.6 Spread of Genes and Traveling Waves 321

    7.7 Pattern Formation 325

    7.8 Integrodifference Equations 330

    7.9 Exercises for Chapter 7 331

    7.10 References for Chapter 7 336

    12.2: Introduction - Biology

    In accordance with Senate's Policy Regarding Inactive Courses, the course descriptions for courses which have not been offered in the previous three academic years and which are not scheduled to be offered in the current academic year have been removed from the following listing. For information about any of these inactive courses, please contact the Head of the Department.

    According to the nature of particular courses, the specified number of laboratory hours may consist of some combination of laboratory work, seminars or directed independent study relevant to the practical aspects of the subject matter.

    Biology courses are designated by BIOL.

    is an introduction to the science of Biology, including a discussion of the unity, diversity and evolution of living organisms.

    is an introduction to the science of Biology, including a discussion of the unity, diversity and evolution of living organisms.

    PR: Science 1807 and Science 1808 BIOL 1001

    is a study of the structure, function and reproductive biology of plants, with emphasis on the vascular plants, and on their relationship to environment and human activities.

    PR: Science 1807 and Science 1808 BIOL 1001 and 1002 Chemistry 1050 (or 1200 or 1010 or the former 1000)

    Modern Biology and Human Society I

    examines various aspects of the human body, and the implications of modern biological research for human beings. Topics include cancer diet and nutrition and associated diseases circulatory disease, immunity, human genetics, biorhythms, new diseases, genetic engineering and reproductive engineering.

    UL: not acceptable as one of the required courses for the Minor, Major or Honours programs in Biology

    Modern Biology and Human Society II

    examines the origins and consequences of the environmental crisis of the 20th century. Topics include the population explosion, energy, material cycles, air and water and land pollution, global food supplies, the fisheries, wildlands, renewable and non-renewable resources, environmental ethics.

    UL: not acceptable as one of the required courses for the Minor, Major or Honours programs in Biology

    Principles of Cell Biology

    is a modern view of the biology of eukaryotic cells, organelles and molecules and their interactions in the functioning of living organisms.

    CO: Physics 1021 or 1051 Biochemistry 2201 or the former 2101

    PR: Physics 1021 or 1051 Biochemistry 2201 or the former 2101

    PR: Science 1807 and Science 1808 BIOL 1001, 1002 and 2250 Chemistry 2400

    Biology for Students of Earth Sciences

    is an introduction of the principles of Biology for students in Earth Sciences. Topics will include principles of classification, levels of biological organization, fundamental characteristics of living organisms and basic concepts in ecology.

    PR: Science 1807 and Science 1808 Earth Science major Earth Sciences 1001 or 1002 or permission of the Head of Department.

    UL: may not be used for credit by Biology Majors or Minors

    is a study of the invertebrates with emphasis on structure and function, adaptations and life histories. The laboratories will present a broad survey of the major invertebrate groups.

    PR: Science 1807 and Science 1808 BIOL 1001, 1002

    is a study of the vertebrates, with emphasis on structure and function, adaptations and life histories.

    PR: Science 1807 and Science 1808 BIOL 1001, 1002

    is an introduction to Mendelian and molecular genetics. Phenotype and genotype, behaviour of alleles in genetic crosses, chromosome theory of inheritance, genetic linkage, molecular biology of DNA, RNA and protein, molecular basis of mutation, recombinant DNA, applications of genetic biotechnology.

    CR: Biochemistry 2100, the former BIOL 3250

    PR: Science 1807 and Science 1808 BIOL 1001 and 1002 Chemistry 1050/1051 (or 1200 and 1001, or 1010 and the former 1011)

    is a conceptual course introducing the principles of ecology, including theoretical, functional and empirical approaches.

    PR: Science 1807 and Science 1808 BIOL 1001 and 1002, or BIOL 2120 and admission to a major in Environmental Physics

    Principles of Evolution and Systematics

    is an introduction to the processes and patterns of evolution, and the principles of classification. Natural selection and other microevolutionary processes, variation and adaptation, species and speciation, phylogenetic systematics, reconstruction of phylogeny, macro-evolutionary patterns in the fossil record and their interpretation.

    CO: Statistics 2550 or any of the courses listed in the credit restrictions of Statistics 2550

    PR: Science 1807 and Science 1808 BIOL 1001, 1002, 2250

    PR: Statistics 2550 or any of the courses listed in the credit restrictions of Statistics 2550

    Biology and Ecology of Boreal and Arctic Seaweeds

    is a field course examination of seaweed biology and ecology with special study of living specimens in estuarine, fiordic and exposed coastal sites, demonstrating their physiological and ecological adaptations to cold-water habitats.

    OR: this course is offered at the Bonne Bay Marine Station during the Summer semester with two weeks of instruction followed by a week to complete course requirements

    PR: Science 1807 and Science 1808 BIOL 2600 or equivalent

    Introduction to Microbiology

    is a course in which the basic principles underlying microbial life are studied. Aspects include structure, function, bioenergetics and growth with an emphasis on prokaryotes. Also studied are viruses, microbial diseases, introductory principles of immunology and the control of microorganisms. The laboratory sessions provide training in culture and determinative techniques using microorganisms.

    PR: Science 1807 and Science 1808 BIOL 1001 and 1002 Biochemistry 2201 or the former 2101

    (same as Biochemistry 3052) is the study of the microbiology of water and food with regard to the beneficial and detrimental roles of microorganisms on interaction with these systems. Emphasis will be on the microbiology of food, fermentations, food spoilage and food borne vectors of human disease.

    CR: Biochemistry 3052 and the former Biochemistry 3054, Biochemistry 3401

    PR: Science 1807 and Science 1808 BIOL 3050

    examines the fundamentals of microbiology with an emphasis on medical microbiology. The course will include topics such as: host responses to infections, human diseases caused by microorganisms, and the control and exploitation of microorganisms.

    PR: Science 1807 and Science 1808 students admitted to the Bachelor of Nursing (Collaborative) program

    UL: not acceptable as one of the required courses for the Minor, Major or Honours programs in Biology, nor is it acceptable for any of the joint programs between Biology and other disciplines

    Insect Morphology and Physiology

    Comparative Vertebrate Anatomy

    examines the phylogenetic development and comparative anatomy of the vertebrates.

    CR: the former BIOL 3200 or the former BIOL 3201

    PR: Science 1807 and Science 1808 BIOL 1001 and 1002

    Population and Evolutionary Ecology

    is an introduction to the theory and principles of evolutionary ecology and population dynamics.

    PR: Science 1807 and Science 1808 BIOL 2600 at least one of BIOL 2010, 2122 or 2210

    is a study of the classification and ecology of insects within an evolutionary framework. Topics will include molecular biological and classical morphological issues surrounding insect taxonomy, evolutionary based higher systematics, and the ecological roles of insects in a variety of ecosystems.

    CR: BIOL 4150 and the former BIOL 4140

    PR: Science 1807 and Science 1808 BIOL 2600. It is recommended that students have successfully completed BIOL 2900

    Comparative Animal Physiology

    is a comparative study of the basic physiological processes, with special attention paid to those strategies invoked by animals which enable them to adapt to environmental changes.

    PR: Science 1807 and Science 1808 BIOL 2060 and 2210

    Principles of Plant Physiology

    is a consideration of the principles of plant physiology, including water relations, nutrition, metabolism, growth and development.

    PR: Science 1807 and Science 1808 BIOL 2010 and 2060

    is a study of microstructure and ultrastructure of tissues and organ systems in vertebrates, particularly mammals, with emphasis on correlating structure and function.

    PR: Science 1807 and Science 1808 BIOL 2060 and 2210

    Molecular and Developmental Biology

    is a study of developmental model systems with a focus on the underlying principles and molecular mechanisms involved in embryogenesis, organogenesis, morphogenesis, cellular differentiation, growth and regeneration in animals (vertebrates and invertebrates) and plants. Current cellular and molecular biology techniques and the implications of developmental biology in modern biological and health research will be emphasized.

    PR: Science 1807 and Science 1808 BIOL 2060 and BIOL 2250 or Biochemistry 2100

    is a study of the principal features of terrestrial ecosystems, with emphasis on the boreal region. This course may be offered in a usual 13 week semester or as a two-week field course.

    LC: either three hours of lecture and three hours of laboratory per week or a two week field course that embodies equivalent instructional time

    LH: either three hours of lecture and three hours of laboratory per week or a two week field course that embodies equivalent instructional time

    PR: Science 1807 and Science 1808 BIOL 2010, 2250, 2600 and 2900 Statistics 2550 or any of the courses listed in the credit restrictions of Statistics 2550

    is the study of the physical, chemical and biological aspects of the freshwater habitat. Topics will include morphometry, light and temperature, water chemistry in relation to nutrients, physiological requirements, composition and interaction of algal and invertebrate populations. Eutrophication, pollution, and environmental changes will also be covered.

    PR: Science 1807 and Science 1808 BIOL 2600

    Environmental Physiology of Animals

    (same as Ocean Sciences 3640) covers physiological adaptations of animals facilitating their survival in natural environments with emphasis on physiological and biochemical responses of animals to extreme environments. Starting with the fundamental basis of physiological mechanisms, the course explores various aspects and the integration of major physiological processes (metabolism, respiration, osmoregulation) and how these relate to ecological niche.

    CR: the former BIOL 3403 or the former BIOL 4455, Ocean Sciences 3640

    PR: BIOL 2060 Biochemistry 3206 or 3106

    UL: may not be used to fulfill the physiology course requirement for a Biology major, honours or joint honours program.

    Field Course in Marine Principles and Techniques

    begins with a two-week field school immediately prior to the beginning of the Fall Semester. In the Fall Semester there are follow-up lectures, readings and submission of reports. The course is designed to introduce the principal marine environments, organisms and techniques. It is strongly recommended that this course be taken before either BIOL 3710, 3711 or 4810.

    PR: Science 1807 and Science 1808 BIOL 2600 Statistics 2550 or any of the courses listed in the credit restrictions of Statistics 2550 and permission of the Head of the Department

    is an introductory course in biotic and abiotic factors controlling marine biomass and primary production, emphasizing plankton and fishes. It introduces students to major groups of marine phytoplankton, zooplankton, and fishes, emphasizing how the physical, chemical, and geological environments interact with biology to define processes and pattern in marine organisms.

    LC: either three hours of lecture and three hours of laboratory per week or a two-week field course that embodies equivalent instructional time

    LH: either three hours of lecture and three hours of laboratory per week or a two-week field course that embodies equivalent instructional time

    PR: Science 1807 and Science 1808 BIOL 2122 and 2600

    Principles of Marine Biology

    is an introductory course in biology of the oceans. Introduces students to marine habitats and the organisms that inhabit them, emphasizing functional morphology, physiology, biodiversity, phylogeny, and ecology. Also includes introduction to marine biogeography, conservation, fisheries and pollution.

    LC: either three hours of lecture and three hours of laboratory per week or a two-week field course that embodies equivalent instructional time

    LH: either three hours of lecture and three hours of laboratory per week or a two-week field course that embodies equivalent instructional time

    PR: Science 1807 and Science 1808 BIOL 2122, BIOL 2600

    examines the biology of the aquatic benthos (bottom-dwelling organisms) their origins, adaptations, life histories and ecological roles. This course may be offered in a usual 13 week semester or as a two-week field course.

    CR: the former Biology 3630

    LC: either three hours of lecture and three hours of laboratory per week or a two-week field course that embodies equivalent instructional time

    LH: either three hours of lecture and three hours of laboratory per week or a two-week field course that embodies equivalent instructional time

    PR: Science 1807 and Science 1808 Biology 2122, 2600 and 3710

    Estuarine Fish Ecology Field Course

    examines community structure, function and distribution of northern coastal fishes in fjords and estuarine environments. Emphasis on sampling, field techniques, taxonomy, quantitative characterization, adaptations and habitat relationships. A comparative approach will contrast fish communities from other areas. To be held as a two week field course.

    PR: Science 1807 and Science 1808 BIOL 2600

    Ecology and Evolution of Fishes

    (same as the former BIOL 4600) examines the evolutionary history and ecology of the world&rsquos fishes, with particular emphasis on those of ecological, economical and cultural importance to Eastern Canada. Topics will include taxonomy, life histories, behaviour, zoogeography, evolutionary ecology, population biology, contemporary evolution, and conservation biology.

    PR: Science 1807 and Science 1808 BIOL 2600 and 2900

    (same as Psychology 3750) is an introduction to the mechanisms, development, function and evolution of behaviour in animals. Topics include the history of ethology and comparative psychology, and behavioural ecology methods of animal behaviour study, behaviour of animals in relation to physiology, learning, communication, mating systems, and other areas in Biology and Psychology.

    PR: BIOL 1001 and 1002 Statistics 2550 or any of the courses listed in the credit restrictions of Statistics 2550

    (same as Earth Sciences 3811) is taught and administered by the Department of Earth Sciences.

    CR: Earth Sciences 3811, the former BIOL 3800, and the former Earth Sciences 3801

    PR: either Earth Sciences 1002 and BIOL 2120 (or BIOL 1001 and 1002) or BIOL 2122 and 2210

    will introduce students to the development of biological understanding, from the classical Greeks to the present. The course consists of an online seminar series, which will cover topics such as the influence of Aristotle, Theophrastus, Hippocrates and Galen, the development of the microscope, the discovery of cells, paleontology, classification, Darwin and evolution, genetics, the discovery of DNA, multidisciplinary approaches to biology, and the impact of biology on everyday life.

    OR: 10 on-line seminars prior to the beginning of the two week field course in Harlow and a two-week field component at Harlow Campus in the Spring semester

    PR: completion of a minimum of 60 credit hours

    UL: not acceptable as one of the required courses for the Minor, Major or Honours programs in Biology

    Research Methods in Genetic Biotechnology

    (same as the former BIOL 4900) will include DNA extraction, DNA amplification by the Polymerase Chain Reaction (PCR), DNA cloning, DNA sequence analysis and Bioinformatics. Additional modules in gene expression and re-sequencing chip technologies may be included. Theory and methods will be introduced in a research framework.

    LH: Three hours of lecture and three hours of laboratory per week or a three week on-campus course that embodies equivalent instructor time

    PR: Science 1807 and Science 1808 BIOL 2060 and 2250

    Introduction to Bioinformatics

    (same as Computer Science 3550) deals with the development and application of computational methods to address biological problems. The course will focus on the fundamental concepts, ideas and related biological applications of existing bioinformatics tools. This course will provide hands-on experience in applying bioinformatics software tools and online databases to analyze experimental biological data, and it will also introduce scripting language tools typically used to automate some biological data analysis tasks.

    PR: Biology 1001 one of COMP 1001, 1002 or 1510 and 6 credit hours in Computer Science or Biology course at the 2000 level or above, excluding Biology 2040, 2041, 2120 or permission of the course instructor

    will examine the ecology and evolution of island life forms, including processes unique to islands, the history of the biological study of islands, types of islands, major island groups, and conservation biology and management of islands, including island restoration and expected impacts of anthropogenic climate change. The island-related biology of Newfoundland will be discussed in detail.

    OR: 3 hours of seminar/discussion group each week

    PR: Science 1807 and Science 1808 BIOL 2900 and 2900

    will examine topics about viruses infecting all forms of life including humans and other animals, plants and bacteria. The scope within the course ranges from the molecular biology of virus replication to virus evolution and ecology. Current issues concerning viruses and society are incorporated into the course including the practical applications of viruses, vaccines, and emerging viruses.

    LH: Three hours of laboratory/seminar/discussion per week

    PR: Science 1807 and Science 1808 BIOL 2900 and 3050

    Advanced Topics in Microbiology

    examines the beneficial and harmful properties of microbes including topics on industrial microbiology and the discovery of new antimicrobial agents. The scope within the course ranges from the genetic manipulation of microbes for useful purposes to the isolation of bacteria for applications in various fields. Current issues concerning microbiology and society will also be discussed including the practical applications of microbes and bacterial diseases affecting society.

    PR: Science 1807 and Science 1808 BIOL 3050

    Fundamentals of Plant Pathology

    provides an introduction to the basic concepts used in the study of plant diseases. Topics will include the different causes and types of plant diseases, mechanisms of plant disease development, pathogen interactions with their hosts and host resistance to pathogens, plant disease epidemiology, and disease management practices. The history and social impacts of plant diseases, as well as current issues in plant health such as food security, will also be covered.

    OR: 3 hour seminar/discussion weekly

    PR: Science 1807 and Science 1808 BIOL 3050

    Advanced Studies in Marine Animal Diversity

    (same as Ocean Sciences 4122) provides an in-depth examination of cellular physiological, behavioural and ecological adaptations in marine animals. Lectures will be combined with discussions of relevant papers from the primary literature on topics of current interest, which may relate to morphology, ecology, evolution, natural history, species interactions and practical applications. Students will also gain hands-on experience by designing and conducting research projects involving live or preserved animals.

    LC: either three hours of lecture and three hours of laboratory per week or a two-week intensive course that embodies equivalent instructional time

    LH: either three hours of lecture and three hours of laboratory per week or a two-week intensive course that embodies equivalent instructional time


    This is a very comprehensive read that provides a solid base in computational biology. The book is structured in 4 parts and 14 chapters which cover all the way from the more basic concepts to advanced material, including the state-of-the-art methodologies in synthetic and systems biology. This is a bedside book for those researchers embarking to do investigation in computational biology and a great office companion for anyone working on systems and synthetic biology.

    -- Rodrigo Ledesma Amaro, Lecturer, Imperial College London

    This is a fantastic book. It offers an elegant introduction to both classical and modern concepts in computational biology. To the uninitiated, it is a terrific first read, bringing alive the glory of the past and the promise of the future. To the interested, it handholds and offers a springboard to dive deep. To the practitioner, it serves as a valuable resource bringing together in a panoramic view many diverse streams that adorn the landscape.

    -- Narendra M. Dixit, Professor, Indian Institute of Science


    An array of approximately 20 types of proteins, called a complement system, is also activated by infection or the activity of the cells of the adaptive immune system and functions to destroy extracellular pathogens. Liver cells and macrophages synthesize inactive forms of complement proteins continuously these proteins are abundant in the blood serum and are capable of responding immediately to infecting microorganisms. The complement system is so named because it is complementary to the innate and adaptive immune system. Complement proteins bind to the surfaces of microorganisms and are particularly attracted to pathogens that are already tagged by the adaptive immune system. This “tagging” involves the attachment of specific proteins called antibodies (discussed in detail later) to the pathogen. When they attach, the antibodies change shape providing a binding site for one of the complement proteins. After the first few complement proteins bind, a cascade of binding in a specific sequence of proteins follows in which the pathogen rapidly becomes coated in complement proteins.

    Complement proteins perform several functions, one of which is to serve as a marker to indicate the presence of a pathogen to phagocytic cells and enhance engulfment. Certain complement proteins can combine to open pores in microbial cell membranes and cause lysis of the cells.

    Chapter 9: Introduction to Molecular Biology

    Figure 9.1 Dolly the sheep was the first cloned mammal. Photo shows Dolly the sheep, which has been stuffed and placed in a glass case.

    The three letters “DNA” have now become associated with crime solving, paternity testing, human identification, and genetic testing. DNA can be retrieved from hair, blood, or saliva. With the exception of identical twins, each person’s DNA is unique and it is possible to detect differences between human beings on the basis of their unique DNA sequence.

    DNA analysis has many practical applications beyond forensics and paternity testing. DNA testing is used for tracing genealogy and identifying pathogens. In the medical field, DNA is used in diagnostics, new vaccine development, and cancer therapy. It is now possible to determine predisposition to many diseases by analyzing genes.

    DNA is the genetic material passed from parent to offspring for all life on Earth. The technology of molecular genetics developed in the last half century has enabled us to see deep into the history of life to deduce the relationships between living things in ways never thought possible. It also allows us to understand the workings of evolution in populations of organisms. Over a thousand species have had their entire genome sequenced, and there have been thousands of individual human genome sequences completed. These sequences will allow us to understand human disease and the relationship of humans to the rest of the tree of life. Finally, molecular genetics techniques have revolutionized plant and animal breeding for human agricultural needs. All of these advances in biotechnology depended on basic research leading to the discovery of the structure of DNA in 1953, and the research since then that has uncovered the details of DNA replication and the complex process leading to the expression of DNA in the form of proteins in the cell.

    Organization of the Nervous System

    As you might predict, the human nervous system is very complex. It has multiple divisions, beginning with its two main parts, the central nervous system (CNS) and the peripheral nervous system (PNS), as shown in the diagram below (Figure 8.2.4). The CNS includes the brain and spinal cord , and the PNS consists mainly of nerves , which are bundles of axons from neurons. The nerves of the PNS connect the CNS to the rest of the body.

    Figure 8.2.4 The two main divisions of the nervous system: the central nervous system (CNS) — which includes the brain and spinal cord — and the peripheral nervous system (PNS), which includes nerves and ganglia (singular, ganglion), which transmit information between the CNS to the rest of the body.

    The PNS can be further subdivided into two divisions, known as the autonomic and somatic nervous system s (Figure 8.2.5 ). These divisions control different types of functions, and they often interact with the CNS to carry out these functions. The somatic nervous system controls activities that are under voluntary control, such as turning a steering wheel. The autonomic nervous system controls activities that are not under voluntary control , such as digesting a meal. The autonomic nervous system has three main divisions: the sympathetic division (which controls the fight-or-flight response during emergencies), the parasympathetic division (which controls the routine “housekeeping” functions of the body at other times), and the enteric division (which provides local control of the digestive system).

    Figure 8.2.5 Divisions of the Nervous System.

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    Biology Details

    Thinkwell's Biology includes:

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      • Evolution
      • Inorganic and organic chemistry
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      • Biotechnology and the Human Genome Project
      • Cell reproduction: mitosis and meiosis
      • Mendelian genetics and mutation
      • Taxonomy and the evolution of Earth's organisms
      • Animal systems such as the skeletal, digestive, and nervous systems
      • Plant systems and photosynthesis
      • Ecology, biomes, and ecosystems

      Table of Contents

      1. Evolution

      • 1.1 Unity and Diversity of Life on Earth
        • 1.1.1 Properties of Life
        • 1.2 Early Perspectives in Science
          • 1.2.1 An Introduction to Biology
          • 1.2.2 The Nature of Science: The Story of Darwin
          • 1.2.3 Early Scientific Thought
          • 1.2.4 The Emerging Science of Geology
          • 1.3 An Introduction to Evolution
            • 1.3.1 Linnaeus, Buffon, and Lamarck
            • 1.3.2 Darwin: The Voyage Continues
            • 1.3.3 Darwin: More Observations
            • 1.4 Evolution: The Theory of Natural Selection
              • 1.4.1 Darwin: The Theory of Natural Selection
              • 1.4.2 The Theory of Natural Selection
              • 1.4.3 Contrasting Lamarck and Darwin
              • 1.4.4 Contrasting Lamarck and Darwin, Part II
              • 1.5 Fossils and Evolution
                • 1.5.1 Fossil Formation, Dating, and Indexing
                • 1.5.2 The Fossil Record
                • 1.5.3 Some Fossil Surprises
                • 1.5.4 The Coevolution of Horses and Plants
                • 1.5.5 Mass Extinctions: An Asteroid Can Ruin Your Day
                • 1.6 Human Evolution
                  • 1.6.1 Human Evolution: What Is a Primate?
                  • 1.6.2 Human Evolution: The Family Tree
                  • 1.6.3 Human Evolution: The Fossil Record
                  • 1.7 Evidence for Evolution
                    • 1.7.1 Evidence for Evolution: Biochemical Similarities
                    • 1.7.2 Evidence for Evolution: Vestigial Structures
                    • 1.7.3 Homologous Structures
                    • 1.8 Species Concepts
                      • 1.8.1 Species Concepts
                      • 1.8.2 Speciation
                      • 1.8.3 Prezygotic Reproductive Isolation
                      • 1.8.4 Postzygotic Reproductive Isolation
                      • 1.9 Examples of Artificial and Natural Selection
                        • 1.9.1 Artificial Selection in Action
                        • 1.9.2 Natural Selection in Action
                        • 1.10 The Origin of Life
                          • 1.10.1 History of Life: The Heterotroph Hypothesis: An Overview
                          • 1.10.2 The Heterotroph Hypothesis: An Introduction
                          • 1.10.3 The Origin of Life: Life from Nonlife
                          • 1.10.4 The Heterotroph Hypothesis: Protobionts
                          • 1.10.5 The Heterotroph Hypothesis: The First Genetic Material
                          • 1.10.6 The Origin of Life: The Rest of the Story
                          • 1.11 Classifying Life
                            • 1.11.1 The Linnaean System
                            • 1.11.2 The Linnaean System: Still Changing

                            2. Inorganic and Organic Chemistry

                            • 2.1 An Introduction to Atoms
                              • 2.1.1 Atomic Structure: SPONCH and the Atom
                              • 2.1.2 Electrons, Orbitals, and Electron Shells
                              • 2.1.3 Ions, Ionization, and Isotopes
                              • 2.1.4 Isotopes: Unraveling Photosynthesis
                              • 2.2 Atoms and Bonding
                                • 2.2.1 Bonding and Electronegativity
                                • 2.2.2 Ionic and Covalent Bonds
                                • 2.2.3 Polar Covalent Bonds, Hydrogen Bonds, and Van der Waals Interactions
                                • 2.3 Properties of Water
                                  • 2.3.1 Water: Hydrogen Bonding, Solubility, and Specific Heat
                                  • 2.3.2 Water: Adhesion, Cohesion, and a Solid That Floats
                                  • 2.3.3 Water: Hydrophilic and Hydrophobic Substances
                                  • 2.3.4 Dissociation of Water and the pH Scale
                                  • 2.3.5 Hemoglobin as a Buffer
                                  • 2.4 Carbon Chemistry
                                    • 2.4.1 Carbon Chemistry and Isomers
                                    • 2.4.2 Functional Side Groups
                                    • 2.5 Carbohydrates
                                      • 2.5.1 Carbohydrates: Monosaccharides
                                      • 2.5.2 Dehydration Synthesis and Hydrolysis: Disaccharides
                                      • 2.5.3 Polysaccharides: Energy Storage Molecules
                                      • 2.5.4 Polysaccharides: Structural Molecules
                                      • 2.6 Lipids and Nucleic Acids
                                        • 2.6.1 Lipids: An Introduction
                                        • 2.6.2 Saturated vs. Unsaturated Fats
                                        • 2.6.3 Phospholipids, Waxes, and Steroids
                                        • 2.6.4 Nucleic Acids: An Introduction to Genetic Material
                                        • 2.7 Proteins
                                          • 2.7.1 Proteins: Amino Acids and the Peptide Bond
                                          • 2.7.2 Amino Acids: The R Groups
                                          • 2.7.3 Primary and Secondary Structure
                                          • 2.7.4 Tertiary Structure
                                          • 2.7.5 Quaternary Structure
                                          • 2.7.6 Protein Structure: A Summary
                                          • 2.8 Enzymes
                                            • 2.8.1 Bioenergetics: The Laws of Thermodynamics
                                            • 2.8.2 Activation Energy
                                            • 2.8.3 Enzyme Characteristics
                                            • 2.9 Enzyme Action
                                              • 2.9.1 Enzyme Action: The Induced-Fit Model
                                              • 2.9.2 Enzyme Regulation: Allosteric Regulation
                                              • 2.9.3 Feedback Inhibition and Cooperativity

                                              3. Cell Biology

                                              • 3.1 An Introduction to Cell Biology
                                                • 3.1.1 The History of Cytology
                                                • 3.1.2 Prokaryotes vs. Eukaryotes
                                                • 3.1.3 Plant and Animal Cell Overview: The Basics
                                                • 3.1.4 Membranes: Basic Structure
                                                • 3.1.5 The Nuclear Envelope: The Initial Tour
                                                • 3.1.6 Nuclear Function: Who's in Charge?
                                                • 3.2 Membrane-Bound Organelles
                                                  • 3.2.1 Cellular Function: Endoplasmic Reticulum
                                                  • 3.2.2 Cell Function: Golgi Apparatus
                                                  • 3.2.3 Food Vacuole Formation: The Role of the Lysosome
                                                  • 3.2.4 Still More Vacuoles and Peroxisomes
                                                  • 3.2.5 Mitochondria: Welcome Guests
                                                  • 3.2.6 The Origin of Mitochondria and Chloroplasts
                                                  • 3.3 The Cytoskeleton
                                                    • 3.3.1 The Cytoskeleton: Basic Components
                                                    • 3.3.2 Centrioles, Flagella, and Cilia
                                                    • 3.3.3 Cell Walls
                                                    • 3.4 The Plasma Membrane
                                                      • 3.4.1 Plasma Membrane: The Extracellular Matrix
                                                      • 3.4.2 The Plasma Membrane: The Fluid-Mosaic Model
                                                      • 3.4.3 Proteins as the Mosaic of the Cell Membrane
                                                      • 3.4.4 Animal Cell Junctions
                                                      • 3.5 Cell Transport
                                                        • 3.5.1 Simple and Facilitated Diffusion
                                                        • 3.5.2 Passive Transport: Osmosis
                                                        • 3.5.3 Active Transport: Ion Pumps and Cotransport
                                                        • 3.5.4 Active Transport: The Sodium-Potassium Pump
                                                        • 3.5.5 Energy-Requiring Transport: Endocytosis and Exocytosis
                                                        • 3.6 Tools for Cell Biology
                                                          • 3.6.1 Tools of the Cytologist: Light and Fluorescent Microscopy
                                                          • 3.6.2 Scanning and Transmission Electron Microscopes
                                                          • 3.6.3 Freeze Fracture and Differential Centrifugation
                                                          • 3.7 The Evolution of Metabolic Functions
                                                            • 3.7.1 Major Modes of Nutrition Among Organisms

                                                            4. Respiration

                                                            • 4.1 An Introduction to Respiration
                                                              • 4.1.1 ATP Structure and Function
                                                              • 4.1.2 Phosphorylated Intermediates
                                                              • 4.1.3 Respiration: An Overview
                                                              • 4.1.4 Redox: A Brief Review
                                                              • 4.1.5 Energy Release from Sugar: A Demo
                                                              • 4.1.6 Coenzymes: The Role of NAD +
                                                              • 4.2 Glycolysis and Fermentation
                                                                • 4.2.1 Glycolysis: The Initial Steps: Energy Input
                                                                • 4.2.2 Glycolysis: The Energy Payoff
                                                                • 4.2.3 Anaerobic Respiration: The Fermentation of Pyruvate
                                                                • 4.3 Aerobic Respiration
                                                                  • 4.3.1 Aerobic Respiration: The Acetyl CoA Step
                                                                  • 4.3.2 Aerobic Respiration: The Krebs Cycle
                                                                  • 4.3.3 Glycolysis and the Krebs Cycle
                                                                  • 4.4 The Electron Transport Chain and Oxidative Phosphorylation
                                                                    • 4.4.1 The Electron Transport Chain
                                                                    • 4.4.2 Oxidative Phosphorylation
                                                                    • 4.4.3 ATP Yield from Aerobic Respiration
                                                                    • 4.4.4 Other Fuels in Respiration
                                                                    • 4.4.5 The Evolution of Glycolysis

                                                                    5. Photosynthesis

                                                                    • 5.1 Discovering Photosynthesis
                                                                      • 5.1.1 The Unraveling of Photosynthesis: A Historical Perspective
                                                                      • 5.1.2 Photosynthesis: Twentieth-Century Breakthroughs
                                                                      • 5.1.3 Photosynthesis: The Final Picture
                                                                      • 5.2 Adaptations for Photosynthesis
                                                                        • 5.2.1 The Leaf: Adaptations for Photosynthesis
                                                                        • 5.2.2 The Structure of a Chloroplast
                                                                        • 5.2.3 Photosynthetic Pigments
                                                                        • 5.2.4 The Nature of Light
                                                                        • 5.2.5 Photoexcitation and Electron Transfer
                                                                        • 5.3 The Light Reactions
                                                                          • 5.3.1 The Light Reactions: An Introduction
                                                                          • 5.3.2 Photosystem 1
                                                                          • 5.3.3 Photosystem 2
                                                                          • 5.3.4 The Light Reactions: A Summary
                                                                          • 5.4 The Dark Reactions
                                                                            • 5.4.1 The Calvin Cycle
                                                                            • 5.4.2 The Calvin Cycle: RuBP Regeneration
                                                                            • 5.4.3 A Review of Photosynthesis
                                                                            • 5.5 Photorespiration
                                                                              • 5.5.1 Photorespiration
                                                                              • 5.5.2 C4 Plants and CAM Plants
                                                                              • 5.5.3 The Evolution of Photosynthesis

                                                                              6. Molecular Genetics

                                                                              • 6.1 Discovering DNA
                                                                                • 6.1.1 Molecular Genetics: The Protein vs. DNA Debate
                                                                                • 6.1.2 Continuing to Link Genes to Chemicals: Muller, Beadle, and Tatum
                                                                                • 6.1.3 Griffith and Transformation
                                                                                • 6.1.4 Avery, MacLeod and McCarty/Hershey and Chase: DNA Wins!
                                                                                • 6.1.5 Chargaff and Franklin and Wilkins: The DNA Story Begins
                                                                                • 6.2 DNA Structure Revealed
                                                                                  • 6.2.1 Watson and Crick: The Clues
                                                                                  • 6.2.2 Watson and Crick: The Double Helix
                                                                                  • 6.3 Introduction to DNA Replication
                                                                                    • 6.3.1 Replication: Meselson and Stahl
                                                                                    • 6.3.2 DNA: Polymerization with Triphosphate Nucleotides
                                                                                    • 6.4 Events of DNA Replication
                                                                                      • 6.4.1 Events at the Replication Fork: The Leading Strand
                                                                                      • 6.4.2 Events at the Leading Strand, Part II
                                                                                      • 6.4.3 Events at the Replication Fork: The Lagging Strand
                                                                                      • 6.4.4 Proofreading, End Replication, and Telomeres
                                                                                      • 6.4.5 DNA Replication: A Summary
                                                                                      • 6.5 Transcription
                                                                                        • 6.5.1 Transcription and Translation: An Overview
                                                                                        • 6.5.2 Transcription: RNA Formation from the DNA Template
                                                                                        • 6.5.3 Transcription: Termination and RNA Protection
                                                                                        • 6.5.4 Posttranscriptional Modification/RNA Splicing
                                                                                        • 6.6 Translation
                                                                                          • 6.6.1 Translation: Ribosomal and Transfer RNA
                                                                                          • 6.6.2 The Role of Transfer RNA: Charging a tRNA Molecule
                                                                                          • 6.6.3 Translation: Initiation Events
                                                                                          • 6.6.4 Translation/Elongation: The Initiation of Elongation
                                                                                          • 6.6.5 Elongation Continued and Termination
                                                                                          • 6.7 Protein Synthesis Review
                                                                                            • 6.7.1 Polypeptide Destinations: Signal Peptides and ER Ribosomes
                                                                                            • 6.7.2 Protein Synthesis: An Overview
                                                                                            • 6.8 The lac Operon
                                                                                              • 6.8.1 Control Mechanisms: Lactose Metabolism in E. coli
                                                                                              • 6.8.2 Jacob and Monod's Model: The lac Operon
                                                                                              • 6.8.3 lac Operon: The Summary
                                                                                              • 6.9 Eukaryotic Genomic Organization
                                                                                                • 6.9.1 The Eukaryotic Genome: DNA Packing
                                                                                                • 6.9.2 Eukaryotic Genomic Organization: Repetitive DNA
                                                                                                • 6.9.3 Eukaryotic Genomic Organization: Gene Families
                                                                                                • 6.9.4 Eukaryotic Genomic Organization: Transposons and Amplified Genes
                                                                                                • 6.10 Controlling Protein Synthesis in Eukaryotes
                                                                                                  • 6.10.1 Eukaryotic Gene Control: Transcriptional Controls
                                                                                                  • 6.10.2 Eukaryotic Control Mechanisms: Posttranscriptional and Posttranslational Controls
                                                                                                  • 6.10.3 Prokaryotes vs. Eukaryotes: Protein-Making Machinery

                                                                                                  7. Biotechnology

                                                                                                  • 7.1 Plasmids and Gene Cloning
                                                                                                    • 7.1.1 Biotechnology: Plasmids in Prokaryotes
                                                                                                    • 7.1.2 Using a Restriction Enzyme to Create a Vector
                                                                                                    • 7.1.3 Biotechnology: Gene Cloning
                                                                                                    • 7.1.4 Biotechnology: Detection of Cell Clones
                                                                                                    • 7.2 Techniques in Biotechnology
                                                                                                      • 7.2.1 Biotechnology: Reverse Transcriptase: A Tool Taken from Viruses
                                                                                                      • 7.2.2 Using Reverse Transcriptase to Make cDNA
                                                                                                      • 7.2.3 Electrophoresis: Separating DNA
                                                                                                      • 7.2.4 Sequencing DNA: The Sanger Method
                                                                                                      • 7.3 More Techniques in Biotechnology
                                                                                                        • 7.3.1 Restriction Fragment Length Polymorphisms: Genetic Markers
                                                                                                        • 7.3.2 Polymerase Chain Reaction: DNA Amplification
                                                                                                        • 7.3.3 DNA Fingerprinting
                                                                                                        • 7.3.4 Southern Blotting
                                                                                                        • 7.3.5 Detecting DNA Homology: A Biotechnology Summary
                                                                                                        • 7.4 Human Genome Project
                                                                                                          • 7.4.1 The Human Gene Pool
                                                                                                          • 7.4.2 The Human Genome Project: Recent Findings

                                                                                                          8. Cell Reproduction

                                                                                                          • 8.1 An Introduction to the Cell Cycle and Mitosis
                                                                                                            • 8.1.1 The Eukaryotic Cell Cycle
                                                                                                            • 8.1.2 Mitosis: An Overview
                                                                                                            • 8.1.3 Mitosis: The Phases
                                                                                                            • 8.1.4 Cytokinesis
                                                                                                            • 8.2 Regulating Mitosis
                                                                                                              • 8.2.1 Cell-Cycle Regulation: Protein Kinases
                                                                                                              • 8.2.2 Cell-Cycle Regulation: Other Mechanisms
                                                                                                              • 8.2.3 Cancer: When Mitosis Goes Unchecked
                                                                                                              • 8.2.4 The ras Gene and the p53 Gene
                                                                                                              • 8.3 Meiosis
                                                                                                                • 8.3.1 Sexual Reproduction and the Role of Meiosis
                                                                                                                • 8.3.2 Homologous Chromosomes: Thanks, Mom and Dad!
                                                                                                                • 8.3.3 Meiosis: Prophase I
                                                                                                                • 8.3.4 Disjunction and Meiosis II
                                                                                                                • 8.3.5 Mitosis vs. Meiosis
                                                                                                                • 8.4 Understanding Meiosis
                                                                                                                  • 8.4.1 Independent Assortment
                                                                                                                  • 8.4.2 Spermatogenesis: Meiosis in Males
                                                                                                                  • 8.4.3 Oogenesis: Meiosis in Females

                                                                                                                  9. Mendelian Genetics and Mutation

                                                                                                                  • 9.1 Gregor Mendel
                                                                                                                    • 9.1.1 Heredity: The Story of Gregor Mendel
                                                                                                                    • 9.1.2 Mendel's Findings: A First Look at Phenotypic Ratios
                                                                                                                    • 9.1.3 Mendel's Conclusions: Alternate Alleles and Dominance
                                                                                                                    • 9.1.4 Mendel's Conclusions: Segregation and Recombination
                                                                                                                    • 9.2 The Laws of Mendelian Inheritance
                                                                                                                      • 9.2.1 Determining Heterozygosity: Test Crosses and Back Crosses
                                                                                                                      • 9.2.2 Mendelian Inheritance
                                                                                                                      • 9.3 Segregation and Independent Assortment
                                                                                                                        • 9.3.1 Segregation and Independent Assortment
                                                                                                                        • 9.3.2 Independent Assortment: An Explanation
                                                                                                                        • 9.4 Laws of Probability
                                                                                                                          • 9.4.1 Laws of Probability: Rule of Multiplication
                                                                                                                          • 9.4.2 The Multiplicative Law: Some Extensions
                                                                                                                          • 9.4.3 Laws of Probability: The Additive Rule
                                                                                                                          • 9.4.4 Using the Laws of Probability in Dihybrid Crosses
                                                                                                                          • 9.5 Genetic Dominance
                                                                                                                            • 9.5.1 What Is a Dominant Gene? Intermediate Inheritance
                                                                                                                            • 9.5.2 Codominance and Multiple Alleles: ABO Blood Genes
                                                                                                                            • 9.5.3 ABO Blood Groups: Inheritance Patterns and Pedigree Charts
                                                                                                                            • 9.6 Epistasis
                                                                                                                              • 9.6.1 Epistasis: One Gene Affecting Another
                                                                                                                              • 9.6.2 The Bombay Phenotype: Infidelity or Epistasis?
                                                                                                                              • 9.7 Inheritance Patterns
                                                                                                                                • 9.7.1 Polygenic Inheritance
                                                                                                                                • 9.7.2 Pleiotropy: Multiple Phenotypic Effects
                                                                                                                                • 9.7.3 Sickle Cell Anemia: The Case against Dominant and Recessive
                                                                                                                                • 9.8 Linked Genes and Genetic Mapping
                                                                                                                                  • 9.8.1 Linked Genes
                                                                                                                                  • 9.8.2 Crossing Over and Recombination: A Tool for Mapping Genes
                                                                                                                                  • 9.8.3 Gene Mapping Using Recombination Frequencies
                                                                                                                                  • 9.8.4 Linking Genes to Chromosomes: The Work of Morgan
                                                                                                                                  • 9.8.5 Morgan's Conclusions
                                                                                                                                  • 9.9 Sex Linkage and Pedigree Charts
                                                                                                                                    • 9.9.1 Sex-Linked Traits in Humans
                                                                                                                                    • 9.9.2 X Inactivation in Humans
                                                                                                                                    • 9.9.3 The Use of Pedigree Charts to Determine Possible Genotypes
                                                                                                                                    • 9.9.4 Pedigree Chart: Problem Review
                                                                                                                                    • 9.10 Problems in Heredity
                                                                                                                                      • 9.10.1 Problems in Heredity
                                                                                                                                      • 9.10.2 Problems in Heredity: Chromosomal Aberrations
                                                                                                                                      • 9.10.3 Translocations: 14/21 Downs
                                                                                                                                      • 9.11 Genetic Mutation
                                                                                                                                        • 9.11.1 Genetic Mutation
                                                                                                                                        • 9.11.2 Genetic Mutation: Different Forms of Point Mutations
                                                                                                                                        • 9.11.3 Genetic Mutation: Insertion and Deletion
                                                                                                                                        • 9.11.4 Genetic Screening

                                                                                                                                        10. Population Genetics and Evolution

                                                                                                                                        • 10.1 The Hardy-Weinberg Theory
                                                                                                                                          • 10.1.1 Population Genetics: Darwin Meets Mendel
                                                                                                                                          • 10.1.2 An Introduction to Hardy-Weinberg Theory
                                                                                                                                          • 10.1.3 The Hardy-Weinberg Equation
                                                                                                                                          • 10.1.4 Using the Hardy-Weinberg Theory
                                                                                                                                          • 10.1.5 Using the Hardy-Weinberg Theory II
                                                                                                                                          • 10.1.6 Hardy-Weinberg: What Does This Have to Do with Evolution?
                                                                                                                                          • 10.2 Departing From Hardy-Weinberg Equilibrium
                                                                                                                                            • 10.2.1 Microevolution by Genetic Drift
                                                                                                                                            • 10.2.2 Microevolution: Continued
                                                                                                                                            • 10.3 Variations in Populations and Modes of Selection
                                                                                                                                              • 10.3.1 Variations Within and Between Populations
                                                                                                                                              • 10.3.2 Modes of Selection
                                                                                                                                              • 10.3.3 The Perfect Organism
                                                                                                                                              • 10.4 Speciation
                                                                                                                                                • 10.4.1 Speciation: What Is a Species?
                                                                                                                                                • 10.4.2 Allopatric Speciation
                                                                                                                                                • 10.4.3 Sympatric Speciation
                                                                                                                                                • 10.5 Evolution
                                                                                                                                                  • 10.5.1 Time Frame for Evolution: Gradualism vs. Punctuated Equilibrium

                                                                                                                                                  11. The Evolution of Life on Earth

                                                                                                                                                  • 11.1 Classifying Earth's Organisms
                                                                                                                                                    • 11.1.1 Classifying the Products of Evolution: Taxonomy
                                                                                                                                                    • 11.1.2 Building a Cladogram
                                                                                                                                                    • 11.1.3 Molecular Methods for Classifying Organisms
                                                                                                                                                    • 11.1.4 A Phylogenetic Tree of Organisms: A Three-Domain System
                                                                                                                                                    • 11.2 Domain Archaea
                                                                                                                                                      • 11.2.1 The Archaea
                                                                                                                                                      • 11.3 Domain Bacteria
                                                                                                                                                        • 11.3.1 The Bacteria
                                                                                                                                                        • 11.4 Protists and the Origin of the Eukaryota
                                                                                                                                                          • 11.4.1 Protists: Archaezoa and Euglenozoa
                                                                                                                                                          • 11.4.2 Protists: Alveolata and Stramenopila
                                                                                                                                                          • 11.5 The Colonization of Land by Plants
                                                                                                                                                            • 11.5.1 Plant Phylogeny: The Colonization of Land
                                                                                                                                                            • 11.5.2 Plant Phylogeny and Alternation of Generations
                                                                                                                                                            • 11.6 Alternation of Generations: Mosses, Ferns, and Gymnosperms
                                                                                                                                                              • 11.6.1 Alternation of Generations: Mosses
                                                                                                                                                              • 11.6.2 Alternation of Generations: Ferns
                                                                                                                                                              • 11.6.3 Alternation of Generations: Gymnosperms
                                                                                                                                                              • 11.7 Angiosperms
                                                                                                                                                                • 11.7.1 Alternation of Generations: The Structure of a Flower
                                                                                                                                                                • 11.7.2 Alternation of Generations: Angiosperms
                                                                                                                                                                • 11.7.3 Embryogenesis in Angiosperms: Dicots and Monocots
                                                                                                                                                                • 11.8 Fungi
                                                                                                                                                                  • 11.8.1 Introduction to the Fungi
                                                                                                                                                                  • 11.8.2 Diversity of Fungi
                                                                                                                                                                  • 11.9 Evolution of the Animal Kingdom
                                                                                                                                                                    • 11.9.1 Constructing a Phylogenetic Tree of Animals: Animal Development
                                                                                                                                                                    • 11.9.2 Developmental Data for the Phylogenetic Tree of Animals
                                                                                                                                                                    • 11.9.3 The Formation of Body Cavities
                                                                                                                                                                    • 11.9.4 Protostomes and Deuterostomes
                                                                                                                                                                    • 11.9.5 Animal Diversity: The Cambrian Explosion and the Move to Land
                                                                                                                                                                    • 11.10 Invertebrates
                                                                                                                                                                      • 11.10.1 Introduction to Animals: Parazoa and Radiata
                                                                                                                                                                      • 11.10.2 Animals: Acoelomates, Pseudocoelomates, and Coelomates
                                                                                                                                                                      • 11.10.3 Diversity of Protostome Species
                                                                                                                                                                      • 11.11 Deuterostomes
                                                                                                                                                                        • 11.11.1 Diversity of Deuterostome Species
                                                                                                                                                                        • 11.11.2 Diversity of Vertebrate Species
                                                                                                                                                                        • 11.12 Chordate Development
                                                                                                                                                                          • 11.12.1 Animal Development: A Close-up Look at Fertilization Events
                                                                                                                                                                          • 11.12.2 Cleavage, Gastrulation, and Organogenesis: A Closer Look
                                                                                                                                                                          • 11.12.3 Events of Gastrulation and Organogenesis
                                                                                                                                                                          • 11.13 The Cellular and Molecular Basis of Development
                                                                                                                                                                            • 11.13.1 Pattern Formation in Drosophila
                                                                                                                                                                            • 11.13.2 Pattern Formation in Drosophila, continued
                                                                                                                                                                            • 11.14 Viruses and Prions
                                                                                                                                                                              • 11.14.1 Viruses and Prions: Living or Nonliving?

                                                                                                                                                                              12. Animal Systems and Homeostasis

                                                                                                                                                                              • 12.1 Introduction to Animal Systems and Homeostasis
                                                                                                                                                                                • 12.1.1 Animal Homeostasis
                                                                                                                                                                                • 12.1.2 Mechanisms of Homeostasis
                                                                                                                                                                                • 12.1.3 Animal Tissues: Epithelial Tissue
                                                                                                                                                                                • 12.1.4 Animal Tissues: Loose Connective Tissue
                                                                                                                                                                                • 12.1.5 Animal Tissues: Dense, Fluid, and Supportive Connective Tissue
                                                                                                                                                                                • 12.1.6 Animal Tissue: Muscle and Nerve Tissue
                                                                                                                                                                                • 12.2 The Digestive System
                                                                                                                                                                                  • 12.2.1 Introduction to the Digestive System
                                                                                                                                                                                  • 12.2.2 The Beginning of Chemical Digestion
                                                                                                                                                                                  • 12.2.3 Chemical Digestion in the Small Intestine
                                                                                                                                                                                  • 12.2.4 Human Nutrition: Absorption
                                                                                                                                                                                  • 12.2.5 Egestion
                                                                                                                                                                                  • 12.3 Gas Exchange and Transport Systems
                                                                                                                                                                                    • 12.3.1 Introduction to the Gas Exchange of Animals
                                                                                                                                                                                    • 12.3.2 Human Gas Exchange System
                                                                                                                                                                                    • 12.3.3 Human Gas Exchange: The Roles of Respiratory Pigments
                                                                                                                                                                                    • 12.3.4 Carbon Dioxide Transport
                                                                                                                                                                                    • 12.3.5 Structure of the Human Heart
                                                                                                                                                                                    • 12.4 Circulation
                                                                                                                                                                                      • 12.4.1 Maintaining the Human Heartbeat
                                                                                                                                                                                      • 12.4.2 Human Circulation: Blood Vessels
                                                                                                                                                                                      • 12.5 Blood Pressure and Clotting
                                                                                                                                                                                        • 12.5.1 Human Circulation: Blood Pressure
                                                                                                                                                                                        • 12.5.2 Blood Clotting
                                                                                                                                                                                        • 12.6 Human Excretion
                                                                                                                                                                                          • 12.6.1 Human Excretion: Waste Processing
                                                                                                                                                                                          • 12.6.2 Human Excretion: Urinary System Structure
                                                                                                                                                                                          • 12.6.3 The Nephron: Blood Filtration and Urine Production
                                                                                                                                                                                          • 12.7 The Immune System: An Introduction
                                                                                                                                                                                            • 12.7.1 The Immune Response: Nonspecific Defenses
                                                                                                                                                                                            • 12.7.2 The Immune System: Structure and Function
                                                                                                                                                                                            • 12.7.3 Immunity: Clonal Selection Theory
                                                                                                                                                                                            • 12.7.4 Immune Response: An Overview
                                                                                                                                                                                            • 12.7.5 T Cells: Helper T Activation
                                                                                                                                                                                            • 12.7.6 T Cells: Helper and Cytotoxic T Cell Effects
                                                                                                                                                                                            • 12.8 The Immune System Continued
                                                                                                                                                                                              • 12.8.1 B Cells: The Humoral Response
                                                                                                                                                                                              • 12.8.2 Antibodies and DNA Rearrangement
                                                                                                                                                                                              • 12.8.3 Antibody Mechanisms
                                                                                                                                                                                              • 12.9 HIV and the Immune System
                                                                                                                                                                                                • 12.9.1 HIV: An Attack on the Immune System
                                                                                                                                                                                                • 12.10 The Endocrine System
                                                                                                                                                                                                  • 12.10.1 Human Regulation: Endocrine Control and Signal-Transduction Pathways
                                                                                                                                                                                                  • 12.10.2 The Endocrine System
                                                                                                                                                                                                  • 12.10.3 Endocrine Function: Oscillations in Hormone Levels
                                                                                                                                                                                                  • 12.11 The Ovarian and Uterine Cycles
                                                                                                                                                                                                    • 12.11.1 The Ovarian and Uterine Cycles: Preparation for Pregnancy
                                                                                                                                                                                                    • 12.11.2 Hormonal Events during the Female Reproductive Cycle
                                                                                                                                                                                                    • 12.12 The Nervous System
                                                                                                                                                                                                      • 12.12.1 The Central and Peripheral Nervous Systems and the Neuron
                                                                                                                                                                                                      • 12.12.2 Human Regulation: Nervous System: Nerve Function and Reflexes
                                                                                                                                                                                                      • 12.13 The Nerve Impulse
                                                                                                                                                                                                        • 12.13.1 Human Regulation: The Nerve Impulse: General Events
                                                                                                                                                                                                        • 12.13.2 Human Regulation: The Nervous System and the Action Potential
                                                                                                                                                                                                        • 12.13.3 Human Regulation: Synaptic Events: Cell-Cell Communication
                                                                                                                                                                                                        • 12.13.4 The Nervous System: A Phylogenetic Perspective
                                                                                                                                                                                                        • 12.13.5 The Human Brain
                                                                                                                                                                                                        • 12.13.6 Processing Centers of the Human Brain
                                                                                                                                                                                                        • 12.14 Motor Mechanisms
                                                                                                                                                                                                          • 12.14.1 Motor Control: Muscle Microstructure
                                                                                                                                                                                                          • 12.14.2 The Neuromuscular Junction: The Contraction Is Triggered
                                                                                                                                                                                                          • 12.14.3 The Sliding Filament: Interaction of ATP, Actin, Myosin, and Calcium
                                                                                                                                                                                                          • 12.15 Sensory Reception
                                                                                                                                                                                                            • 12.15.1 Sensory Systems: An Introduction
                                                                                                                                                                                                            • 12.15.2 Photoreceptors and the Vertebrate Eye
                                                                                                                                                                                                            • 12.15.3 The Ear and Equilibrium
                                                                                                                                                                                                            • 12.15.4 The Ear and Hearing

                                                                                                                                                                                                            13. Plant Systems and Homeostasis

                                                                                                                                                                                                            • 13.1 Plant Development
                                                                                                                                                                                                              • 13.1.1 Plant Development: Germination
                                                                                                                                                                                                              • 13.1.2 Plant Development: Cell Structure and Function
                                                                                                                                                                                                              • 13.1.3 Primary Growth: Root Growth and Development
                                                                                                                                                                                                              • 13.1.4 Primary Growth: Stem Growth and Development
                                                                                                                                                                                                              • 13.1.5 Secondary Growth: Lateral Meristems and Secondary Vascular Tissue
                                                                                                                                                                                                              • 13.2 Plant Hormones
                                                                                                                                                                                                                • 13.2.1 Regulation in Plants
                                                                                                                                                                                                                • 13.2.2 Plant Hormones
                                                                                                                                                                                                                • 13.2.3 Signal Transduction Pathways in Plants
                                                                                                                                                                                                                • 13.3 Photoperiodism
                                                                                                                                                                                                                  • 13.3.1 Photoperiodism in Plants: Control of Flowering
                                                                                                                                                                                                                  • 13.3.2 Phytochromes and the Photoperiodic Response
                                                                                                                                                                                                                  • 13.4 Plant Transport
                                                                                                                                                                                                                    • 13.4.1 Transport in Angiosperms: Transpiration
                                                                                                                                                                                                                    • 13.4.2 The Role of Xylem Tissue and Stomata
                                                                                                                                                                                                                    • 13.4.3 Plant Transport: Absorption and Lateral Transport in Roots
                                                                                                                                                                                                                    • 13.4.4 Phloem: The Movement of Sap

                                                                                                                                                                                                                    14. Ecology

                                                                                                                                                                                                                    • 14.1 Introduction to Ecology
                                                                                                                                                                                                                      • 14.1.1 Ecological Organization: The Functional Divisions of the Ecologist
                                                                                                                                                                                                                      • 14.2 Biomes
                                                                                                                                                                                                                        • 14.2.1 Land Biomes: An Overview
                                                                                                                                                                                                                        • 14.2.2 Terrestrial Biomes: Water-Limited Environments
                                                                                                                                                                                                                        • 14.2.3 Aquatic Biomes
                                                                                                                                                                                                                        • 14.3 Animal Behavior
                                                                                                                                                                                                                          • 14.3.1 Ecology at the Level of the Species: Behavior
                                                                                                                                                                                                                          • 14.3.2 Imprinting and Innate Behavior
                                                                                                                                                                                                                          • 14.3.3 Nature vs. Nurture: Is There a Genetic Basis for Behaviors?
                                                                                                                                                                                                                          • 14.4 Competitive and Courtship Behaviors
                                                                                                                                                                                                                            • 14.4.1 Competitive Behaviors and Survivability
                                                                                                                                                                                                                            • 14.4.2 Courtship and Mating Behaviors: Survivability
                                                                                                                                                                                                                            • 14.5 Population Ecology
                                                                                                                                                                                                                              • 14.5.1 Population Ecology: Populations with Unlimited Resources
                                                                                                                                                                                                                              • 14.5.2 Population Ecology: The Reality of Limited Resources
                                                                                                                                                                                                                              • 14.5.3 Population Ecology: Population Strategy: r vs. K
                                                                                                                                                                                                                              • 14.5.4 Population Ecology: Intraspecific Competition
                                                                                                                                                                                                                              • 14.6 Community Ecology: Interspecific Interactions
                                                                                                                                                                                                                                • 14.6.1 Community Ecology: Interspecific Interaction: Predation
                                                                                                                                                                                                                                • 14.6.2 Interspecific Competition: Ecological Niches
                                                                                                                                                                                                                                • 14.6.3 Interspecific Associations: Symbiosis
                                                                                                                                                                                                                                • 14.7 Community Ecology: Succession
                                                                                                                                                                                                                                  • 14.7.1 Community Disturbance: Succession
                                                                                                                                                                                                                                  • 14.7.2 Secondary Succession
                                                                                                                                                                                                                                  • 14.8 Community Ecology: Species Diversity
                                                                                                                                                                                                                                    • 14.8.1 The Decline in Species Diversity and the Current Mass Extinction
                                                                                                                                                                                                                                    • 14.9 Energy Flow in an Ecosystem
                                                                                                                                                                                                                                      • 14.9.1 Ecosystems: A Flow of Energy
                                                                                                                                                                                                                                      • 14.9.2 Ecosystems: Productivity and Energy Flow
                                                                                                                                                                                                                                      • 14.9.3 Productivity Pyramids: Visualizing Energy Flows
                                                                                                                                                                                                                                      • 14.9.4 Productivity Pyramids: Pyramid of Numbers
                                                                                                                                                                                                                                      • 14.10 Chemical Cycling in the Ecosystem
                                                                                                                                                                                                                                        • 14.10.1 Ecosystems and Material Cycles: Water, Carbon, and Sulfur
                                                                                                                                                                                                                                        • 14.10.2 Ecosystems and Material Cycles: Nitrogen and Phosphorus Cycles
                                                                                                                                                                                                                                        • 14.11 Human Effect on the Ecosystem
                                                                                                                                                                                                                                          • 14.11.1 The Effects of Human Population Growth: Lake Eutrophication
                                                                                                                                                                                                                                          • 14.11.2 Toxic Accumulation and Ozone Depletion

                                                                                                                                                                                                                                          About the Author

                                                                                                                                                                                                                                          George Wolfe
                                                                                                                                                                                                                                          Loudon County Schools Academy of Science

                                                                                                                                                                                                                                          George Wolfe brings 30+ years of teaching and curriculum writing experience to Thinkwell Biology. His teaching career started in Zaire, Africa where he taught Biology, Chemistry, Political Economics, and Physical Education in the Peace Corps. He returned to the U.S. and spent 20 years teaching in the Rochester City School District. He is now the Director of the Loudoun Academy of Science, a magnet school for science and technology that he helped create.

                                                                                                                                                                                                                                          Besides his teaching career, Mr. Wolfe has also been an Emmy-winning television host, fielding live questions for the PBS/WXXI production of Homework Hotline as well as writing and performing in "Football Physics" segments for the Buffalo Bills and the Discover Channel.

                                                                                                                                                                                                                                          His contributions to education have been extensive, serving on multiple advisory boards including the Cornell Institute of Physics Teachers, the Cornell Institute of Biology Teachers and the Harvard-Smithsonian Center for Astrophysics SportSmarts curriculum project. He has authored several publications including "The Nasonia Project", a lab series built around the genetics and behaviors of a parasitic wasp.

                                                                                                                                                                                                                                          He has received numerous awards throughout his teaching career including the NSTA Presidential Excellence Award, The National Association of Biology Teachers Outstanding Biology Teacher Award for New York State, The Shell Award for Outstanding Science Educator, and was recently inducted in the National Teaching Hall of Fame.

                                                                                                                                                                                                                                          Watch the video: Chapter 12 Ex Introduction to Three Dimensional Geometry. Class 11 Maths. Ncert (February 2023).