Jacaranda Nature of Biology 2: VCE Units 3 & 4

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Title page Copyright page Contents About this resource Accessing online resources Acknowledgements Topic 1: The relationship between nucleic acids and proteins 1.1 Overview 1.1.1 Introduction 1.2 BACKGROUND KNOWLEDGE Reviewing cells 1.2.1 What are cells? 1.2.2 Comparing eukaryotic and prokaryotic cells 1.2.3 Organelles 1.2.4 The plasma membrane 1.3 Nucleic acids as information molecules 1.3.1 What are nucleic acids? 1.3.2 The structure of DNA 1.3.3 Forms of RNA 1.4 The genetic code and protein synthesis 1.4.1 Features of the genetic code 1.4.2 Steps in gene expression 1.4.3 Transcription 1.4.4 RNA processing in eukaryotic cells 1.4.5 Translation 1.5 The structure of genes 1.5.1 The structure of genes 1.5.2 Exons and introns 1.5.3 Promoter regions — upstream 1.5.4 Operator regions 1.6 Gene regulation 1.6.1 Types of genes 1.6.2 The trp operon 1.7 Amino acids and polypeptides 1.7.1 Structure of amino acids 1.7.2 Formation of a polypeptide chain 1.7.3 Hierarchical structure of a functional protein 1.8 The proteome 1.8.1 The diversity of proteins 1.8.2 What is the proteome? 1.9 Organelles involved in the protein secretory pathway 1.9.1 Ribosomes 1.9.2 Rough endoplasmic reticulum 1.9.3 Golgi apparatus 1.9.4 Vesicles 1.10 Review Topic 2: DNA manipulation techniques and applications 2.1 Overview 2.1.1 Introduction 2.2 The use of enzymes to manipulate DNA 2.2.1 Polymerase to synthesise DNA 2.2.2 Endonucleases to cut DNA 2.2.3 Ligase to join DNA 2.3 CRISPR-Cas9 2.3.1 The function of CRISPR-Cas9 in bacteria 2.3.2 Application of CRISPR-Cas9 2.4 Amplification of DNA using polymerase chain reaction 2.5 The use of gel electrophoresis 2.5.1 Using gel electrophoresis to sort fragments 2.5.2 Why do we conduct DNA profiling? 2.5.3 Which DNA is used for identification? 2.5.4 Interpretation of gel runs for DNA profiling 2.6 Recombinant plasmids 2.6.1 Making recombinant plasmids 2.6.2 Getting plasmids into bacterial cells 2.6.3 Producing human insulin 2.7 The use of genetically modified and transgenic organisms 2.7.1 Distinction between genetically modified and transgenic organisms 2.7.2 Applications in agriculture 2.7.3 Increased productivity and resistance to disease 2.8 Review UNIT 3: AREA OF STUDY 1 - What is the role of nucleic acids and proteins in maintaining life? UNIT 3: AREA OF STUDY 1 - PRACTICE SCHOOL-ASSESSED COURSEWORK Topic 3 Regulation of biochemical pathways 3.1 Overview 3.1.1 Introduction 3.2 Biochemical pathways 3.2.1 What are biochemical pathways? 3.2.2 Types of biochemical pathways 3.3 The role of enzymes in biochemical pathways 3.3.1 The role of enzymes 3.3.2 The features of enzymes 3.3.3 Types of enzymes 3.3.4 Enzymes involved in photosynthesis 3.3.5 Enzymes involved in cellular respiration 3.3.6 Case studies of enzymes 3.4 The role of coenzymes in biochemical pathways 3.4.1 What are coenzymes? 3.4.2 The role of coenzymes in biochemical pathways 3.4.3 Coenzymes involved in cellular respiration 3.4.4 Coenzymes involved in photosynthesis 3.5 Factors that impact enzyme function 3.5.1 Effect of temperature on enzyme activity 3.5.2 Effect of pH on enzyme activity 3.5.3 Substrate concentration 3.5.4 Enzyme concentration 3.5.5 Competitive inhibitors 3.5.6 Non-competitive inhibitors 3.5.7 Regulation of biochemical pathways 3.6 Review Topic 4 Photosynthesis, cellular respiration and biotechnological applications 4.1 Overview 4.1.1 Introduction 4.2 Photosynthesis 4.2.1 Role of photosynthesis 4.2.2 Biochemical pathway of photosynthesis 4.2.3 The chloroplast: the location of photosynthesis 4.2.4 Light-dependent stage of photosynthesis 4.2.5 Light-independent stage or Calvin cycle 4.2.6 The two stages of the photosynthesis pathway are linked 4.3 Adaptations in C3, C4 and CAM plants 4.3.1 C3, C4 and CAM plants 4.3.2 Photorespiration in C3 plants: it’s all about Rubisco 4.3.3 Mechanisms to prevent photorespiration in C4 plants 4.3.4 Mechanisms to prevent photorespiration in CAM plants 4.3.5 Comparing photosynthesis in C3, C4 and CAM plants 4.4 Factors that affect the rate of photosynthesis 4.4.1 Light availability 4.4.2 Water availability 4.4.3 Temperature 4.4.4 Carbon dioxide concentration 4.4.5 Interrelationship between various factors 4.5 Cellular respiration 4.5.1 Role of cellular respiration 4.5.2 Biochemical pathway of aerobic cellular respiration 4.5.3 Glycolysis — the first stage of aerobic cellular respiration 4.5.4 The mitochondria 4.5.5 Krebs cycle — the second stage of aerobic cellular respiration 4.5.6 Electron transport chain — the third stage of aerobic cellular respiration 4.5.7 Putting the three stages together 4.6 Anaerobic fermentation 4.6.1 Role of anaerobic fermentation 4.6.2 Biochemical pathway of anaerobic fermentation 4.6.3 Anaerobic fermentation in animals 4.6.4 Anaerobic fermentation in yeasts 4.6.5 Comparing cellular respiration and fermentation 4.7 Factors that affect the rate of cellular respiration 4.7.1 Temperature 4.7.2 Glucose concentration 4.7.3 Oxygen concentration 4.8 Improving photosynthetic efficiencies and crop yields using CRISPR-Cas9 4.8.1 Applications of CRISPR-Cas9 in plant breeding 4.9 Uses and applications of the anaerobic fermentation of biomass 4.9.1 Reviewing the applications of anaerobic fermentation 4.9.2 What is biomass? 4.9.3 The anaerobic fermentation of biomass and applications 4.9.4 Applications and uses of biomass 4.9.5 Sustainability and biofuel production 4.10 Review UNIT 3: AREA OF STUDY 2 - How are biochemical pathways regulated? UNIT 3: AREA OF STUDY 2 - PRACTICE SCHOOL-ASSESSED COURSEWORK Topic 5 Responding to antigens and acquiring immunity 5.1 Overview 5.1.1 Introduction 5.2 Antigens, pathogens and allergens 5.2.1 Antigens 5.2.2 Pathogens — sources of non-self antigens 5.2.3 Cellular pathogens 5.2.4 Non-cellular pathogens 5.2.5 Allergens 5.3 Subdivisions of immunity 5.3.1 Innate immunity 5.3.2 Adaptive immunity 5.3.3 Cell-mediated and humoral responses 5.3.4 Lines of defence 5.4 Physical, chemical and microbiota barriers 5.4.1 Physical barriers in animals 5.4.2 Chemical barriers in animals 5.4.3 Microbiological barriers in animals 5.4.4 Barriers in plants 5.5 The components of innate immunity 5.5.1 What is the innate immune response? 5.5.2 Cells involved in innate immunity 5.5.3 Phagocytes and phagocytosis 5.5.4 Macrophages 5.5.5 Neutrophils 5.5.6 Dendritic cells 5.5.7 Eosinophils 5.5.8 Natural killer (NK) cells 5.5.9 Mast cells 5.5.10 Humoral innate immunity 5.5.11 Complement proteins 5.5.12 Interferons 5.6 The inflammatory response in innate immunity 5.6.1 What is inflammation? 5.6.2 Stages of inflammation 5.7 The role of the lymphatic system 5.7.1 The function of the lymphatic system 5.7.2 Lymphatic system structure 5.8 Initiation of an adaptive immune response 5.8.1 Initiating the adaptive immune system 5.8.2 Helper T cells 5.9 The adaptive immune response 5.9.1 Features of adaptive immune response 5.9.2 Components of adaptive immune response 5.10 Humoral adaptive immunity and B lymphocytes 5.10.1 What is the humoral adaptive immune response? 5.10.2 Activating the humoral adaptive response 5.10.3 Antibody structure and function 5.11 Cell-mediated adaptive immunity and cytotoxic T cells 5.11.1 What is cell-mediated immunity? 5.11.2 Cytotoxic T cells (TC) 5.11.3 Activating the cell-mediated adaptive response 5.11.4 Apoptosis and cytotoxic T cells 5.12 Natural and artificial immunity 5.12.1 Types of acquired immunity 5.12.2 Active immunity 5.12.3 Passive immunity 5.13 Review Topic 6: Disease challenges and strategies 6.1 Overview 6.1.1 Introduction 6.2 The emergence and re-emergence of pathogens 6.2.1 Different types of diseases 6.2.2 Pathogens, pandemics and epidemics 6.2.3 The impact of European arrival on Aboriginal and Torres Strait Islander peoples 6.3 Identifying and controlling the spread of pathogens 6.3.1 Bringing outbreaks under control 6.3.2 Identifying pathogens 6.3.3 Identifying the host 6.3.4 Modes of pathogen transmission 6.3.5 Measuring the spread of a pathogen 6.3.6 Controlling the spread of pathogens 6.4 Vaccination programs and herd immunity 6.4.1 Vaccination programs 6.4.2 The importance of mass vaccination 6.4.3 Herd immunity 6.5 Development of immunotherapy strategies 6.5.1 What is immunotherapy? 6.5.2 What are monoclonal antibodies? 6.5.3 Use of monoclonal antibodies to treat cancer 6.5.4 Use of monoclonal antibodies to treat autoimmune diseases 6.6 Review UNIT 4: AREA OF STUDY 1 - How do organisms respond to pathogens? UNIT 4: AREA OF STUDY 1 - PRACTICE SCHOOL-ASSESSED COURSEWORK Topic 7: Genetic changes in a population over time 7.1 Overview 7.1.1 Introduction 7.2 Gene pools and allele frequencies 7.2.1 What are gene pools? 7.2.2 Allele frequencies in a population 7.3 Environmental selection pressures, genetic drift and gene flow 7.3.1 Environmental selection pressures and natural selection 7.3.2 Genetic drift 7.3.3 Gene flow 7.4 Mutations as the source of new alleles 7.4.1 Mutations as a source of new alleles 7.4.2 Causes of mutation 7.4.3 Types of mutation 7.4.4 Point mutations 7.4.5 Substitution mutations 7.4.6 Frameshift mutations 7.4.7 Other types of mutations 7.5 Biological consequences of changing allele frequencies 7.5.1 Genetic diversity within populations 7.5.2 Biological consequences of low genetic diversity 7.5.3 Protecting genetic diversity 7.6 Selective breeding programs 7.6.1 What is selective breeding? 7.6.2 The effect of selective breeding on gene pools 7.7 The consequences of rapid genetic change in pathogens 7.7.1 Consequences of bacterial resistance 7.7.2 Consequences of antigenic shift and drift in viruses 7.8 Review Topic 8: Changes in species over time 8.1 Overview 8.1.1 Introduction 8.2 Changes in species over geological time 8.2.1 Geological time 8.2.2 Changing life forms over time evidenced with fossils 8.2.3 Types of fossils 8.2.4 Formation of fossils 8.3 Evidence from fossils 8.3.1 Evidence from fossils 8.3.2 Faunal succession 8.3.3 Index and transitional fossils 8.3.4 Dating fossils 8.4 Speciation 8.4.1 What is speciation? 8.4.2 Allopatric speciation 8.4.3 Sympatric speciation 8.5 Review Topic 9: Determining the relatedness over time 9.1 Overview 9.1.1 Introduction 9.2 Structural morphology 9.2.1 What does it mean to be related? 9.2.2 Homologous structures 9.2.3 Vestigial structures 9.3 Molecular homology 9.3.1 Comparing amino acid sequences 9.3.2 Comparing DNA 9.4 Phylogenetic trees 9.4.1 What are phylogenetic trees? 9.4.2 Components of phylogenetic trees 9.4.3 Drawing phylogenetic trees 9.5 Review Topic 10: Human change over time 10.1 Overview 10.1.1 Introduction 10.2 Shared characteristics of mammals, primates, hominoids and hominins 10.2.1 Shared characteristics of mammals 10.2.2 Shared characteristics of primates 10.2.3 Shared characteristics of hominoids 10.2.4 Shared characteristics of hominins 10.3 Major trends in hominin evolution 10.3.1 Major trends in hominin evolution 10.3.2 Changes in brain size 10.3.3 Changes in limb structure 10.3.4 A detailed look at members of the early hominin tribe 10.3.5 A detailed look at members of the genus Homo 10.4 Interpretation of the human fossil record 10.4.1 The changing classification schemes around evolution 10.4.2 The human fossil record is always changing 10.4.3 Evidence of interbreeding between Homo sapiens and Homo neanderthalensis 10.4.4 Evidence of new putative Homo species 10.5 Evidence of the migration of modern human populations 10.5.1 Migration of modern humans 10.5.2 Evidence of migration 10.5.3 Migration of Aboriginal and Torres Strait Islander populations 10.6 Review UNIT 4: AREA OF STUDY 2 - How are species relatedover time? UNIT 4: AREA OF STUDY 2 - PRACTICE SCHOOL-ASSESSED COURSEWORK Topic 11: Scientific investigations 11.1 Overview 11.1.1 Introduction 11.2 Key science skills and concepts in biology 11.2.1 The scientific method — why do we conduct investigations? 11.2.2 Using a logbook 11.2.3 Independent, dependent and controlled variables 11.2.4 Developing questions and aims 11.2.5 Formulating hypotheses and making predictions 11.2.6 Biological concepts specific to an investigation 11.3 Characteristics of scientific methodology and primary data generation 11.3.1 Types of scientific investigation methodologies 11.3.2 Characteristics of scientific method 11.3.3 Designing an investigation 11.3.4 Appropriate use of variables in scientific investigations 11.3.5 Selecting appropriate equipment and techniques 11.3.6 Conducting investigations 11.3.7 Generating and collecting primary data 11.3.8 Adapting and extending processes in investigations 11.4 Health, safety and ethical guidelines 11.4.1 Health and safety guidelines 11.4.2 Ethical guidelines 11.5 Accuracy, precision, reproducibility, repeatability and validity of measurements 11.5.1 Accuracy and precision 11.5.2 Repeatability and reproducibility 11.5.3 Validity 11.6 Ways of organising, analysing and evaluating primary data 11.6.1 Organising primary data 11.6.2 Analysing primary data 11.6.3 Evaluating primary data 11.6.4 Sources of error and uncertainty 11.7 The nature of evidence and key findings and implications of investigations 11.7.1 Strong and weak evidence 11.7.2 Distinguishing between opinion, anecdote and evidence, and scientific and non-scientific ideas 11.7.3 Using evidence to support or refute a hypothesis, model or theory 11.7.4 Key findings and implications of investigations and drawing conclusions 11.8 Assumptions and limitations of investigation methodology and conclusions 11.8.1 Limitations and assumptions in scientific methodologyand methods 11.8.2 Limitations and assumptions in data 11.8.3 Limitations in models and theories 11.8.4 Limitations in conclusions 11.9 Conventions of science communication 11.9.1 Why is communication important? 11.9.2 Using terminology and representations 11.9.3 Symbols and formulas in biology 11.9.4 Standard abbreviations 11.9.5 Units of measurement 11.10 Conventions of scientific poster presentation 11.10.1 Conventions of scientific reporting 11.10.2 Referencing and acknowledgment of sources 11.10.3 Producing a scientific poster 11.10.4 Reviewing your investigation 11.11 Review UNIT 4: AREA OF STUDY 3 - How is scientific inquiry used to investigate cellular processes and/or biological change? GLOSSARY