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BIOLOGY SEMESTER ONE COURSE OUTLINE BIOLOGY: SEMESTER ONE: COURSE OUTLINE Welcome to Introduction to Biology (Semester 1)! This Outline includes information about the learning outcomes, delivery, scheduling, assessments and resources required for this course. COURSE DESCRIPTION This science major course is designed to provide students with a foundation for biology. Topics include chemistry related to biological processes, cellular structure and function, photosynthesis, cellular reproduction, genetics, inheritance, protein synthesis, and biotechnology. Course material is closely correlated with the textbook (Biology, by Reece et al., 2011). The course includes extensive laboratory components which are designed to be completed with several different delivery strategies: at-home lab kits, field trips to local environments, and access to the Remote Web-based Science Laboratory (RWSL). LEARNING OUTCOMES Introduction to Biology is an introductory course in general Biology which will prepare you for more advanced and specialized courses in Biological, Ecological, Environmental, and Health Sciences. Subjects covered in this term include genetics, evolution, taxonomy and classification of organisms, and ecology. Upon completion of the course, you will be able to: base your understanding of biological processes on a foundational understanding of chemistry consider how the unique properties of water and carbon are responsible for maintaining and defining living systems differentiate between the major classes of macromolecules and the role they play in living systems use a microscope to identify and study cellular structures understand the importance of cell membranes in regulating the physiology of the cell relate chemical and physical processes to the metabolism of the cell Understand similarities and differences between cellular respiration and fermentation Consider how physical, chemical and biological processes work together in the process of photosynthesis Relate chemical signalling to cellular response Relate the events of mitosis and meiosis to their specific purposes in the cell life cycle Use Mendelian genetics to predict the outcomes of genetic crosses Use the chromosome theory of inheritance to analyze patterns of inherited characteristics Understand how genetic transcription occurs at the molecular level and apply this understanding to protein construction and construction 'errors' Creative Commons Attribution 3.0 Unported License 1 BIOLOGY SEMESTER ONE COURSE OUTLINE Apply your knowledge about gene expression to understand variations in development and factors in disease Develop an informed perspective on a variety of current topics in biotechnology Use laboratory techniques to explore basic biological principles practise basic techniques and analyses for genetic engineering For a more detailed list of course learning objectives, see Appendix A. PREREQUISITES Biology 12 or ABE Provincial Level Biology (C+ minimum) and Principles of Math 12 or ABE Provincial Level Math (C minimum). Chemistry 11 or ABE Advanced Chemistry is recommended. REQUIRED MATERIALS/TEXTS Biology, Campbell & Reece, 2011, 9th Edition Access to Mastering Biology website (http://www.masteringbiology.com/)- access is included with purchase of the textbook. Dictionary of Biology by Abercromble, Hickman, and Johnson (optional) Photographic Atlas for laboratories (optional) EVALUATION PROFILE Laboratories and Assignments……………………………………………… 40% Midterms................................................................................ 25% Final ........................................................................................ 35% TOTAL.................................................................................100% GETTING STARTED This course has been organized by textbook chapter (as listed in Reece et al., 2011) and is designed to be completed over a 15-16 week semester. Each unit includes: Introductory material List of Learning Objectives to guide your study Supplementary material (any or all of Key Terms, Root Words to Know, Useful Resources) A “check list” detailing what you must do to complete the unit Assignments Creative Commons Attribution 3.0 Unported License 2 BIOLOGY SEMESTER ONE COURSE OUTLINE To begin each week, review the checklist to acquire a list of your weekly readings and assignments. Then review the vocabulary lists and links to resources that are intended to increase your understanding of the topics. Any references to Video Clips or Discovery Videos can be found on the Mastering Biology Website that accompanies your textbook. There are many more resources on this site, including practice questions, tutorials, videos, and diagrams. It is a great resource if you are looking for more explanations or practice for course topics. It also gives you access to the complete textbook in digital format if you prefer reading from your computer. COURSE THEORY PROPOSED SCHEDULE Topic Week 1 Chapter Reading Campbell & Reece (9th Ed) Chapters 1 & 2 Week 6 Course Introduction The Chemical Context of Life Water and the Fitness of the Environment Carbon and the Molecular Diversity of Life The Structure and Function of Large Biological Molecules A Tour of the Cell Membrane structure and Function An Introduction to Metabolism Cellular Respiration: Harvesting Chemical Energy Photosynthesis Midterm Exam Review Midterm Exam I Week 7 Cell Communication Chapter 11 Week 8 The Cell Cycle Chapter 12 Week 9 Meiosis and Sexual Life Cycles Mendel and the Gene Idea Mendel and the Gene Idea (cont’d) The Chromosomal Basis of Inheritance The Chromosomal Basis of Inheritance (cont’d) Midterm Review Midterm Exam II Chapters 13 & 14 The Molecular Basis of Inheritance From Gene to Protein Chapters 16 & 17 Week 2 Week 3 Week 4 Week 5 Week 10 Week 11 Week 12 Week 13 Creative Commons Attribution 3.0 Unported License Chapters 3, 4 & 5 Chapters 6 & 7 Chapters 8 & 9 Chapter 10 Chapters 14 & 15 Chapters 15 & 16 3 BIOLOGY SEMESTER ONE COURSE OUTLINE Week 14 Week 15 Week 16 From Gene to Protein (cont’d) Regulation of Gene Expression Biotechnology Exam Review Final Exam Creative Commons Attribution 3.0 Unported License Chapters 17 & 18 Chapter 20 4 BIOLOGY SEMESTER ONE COURSE OUTLINE COURSE LAB SCHEDULE Week Lab Topic Delivery Type Week 2 Introduction to the Scientific Method and Microscopy RWSL and kit-based lab Week 3 Chemistry/ Biomolecules Kit-based lab Week 4 Cell Lab: varieties of cells from a Kingdom perspective RWSL Week 5 Membrane Transport & Tonicity Kit-based lab Week 7 pH Kit-based lab Week 8 Enzymes Kit-based lab Week 9 Photosynthesis Kit-based lab Week 10 Cellular respiration Kit-based lab Week 11 Mendelian genetics Simulation Week 13 Mitosis & Meiosis RWSL and kit-based lab Week 14 DNA/Biotechnology RWSL Creative Commons Attribution 3.0 Unported License 5 BIOLOGY SEMESTER ONE COURSE OUTLINE APPENDIX A: DETAILED LEARNING OBJECTIVES Unit 1 Learn the hierarchy of structural levels in biological organization. Understand how novel properties of life emerge from complex organization. Identify characteristics shared by all cells. Distinguish between prokaryotic and eukaryotic cells. Understand the basic structure and function of DNA. Understand the importance of regulatory mechanisms in living things, and distinguish between positive and negative feedback. Distinguish among the three domains of life, and among the three kingdoms of multicellular, eukaryotic life. Distinguish between discovery and hypothesis-based science, between inductive and deductive reasoning and between quantitative and qualitative data. Understand why hypotheses must be testable and falsifiable, but are never provable. Understand the elements of experimental design. Unit 2 Understand atoms, elements, compounds, and how their properties enable living things. Explain how the atomic number and mass number of an atom can be used to determine the number of neutrons. Explain how two isotopes of an element are similar, and how they differ. Define the terms energy and potential energy. Explain why electrons in the first electron shell have less potential energy than electrons in higher electron shells. Distinguish between nonpolar covalent, polar covalent and ionic bonds, and explain how both strong covalent bonds and weak bonds are essential in living organisms. Explain what is meant by a chemical equilibrium. Unit 3 Using diagrams, explain why water molecules are: o Polar; o capable of hydrogen bonding with four neighbouring water molecules. List four characteristics of water that are emergent properties resulting from hydrogen bonding. Define cohesion and adhesion. Explain how water’s cohesion and adhesion contribute to the movement of water from the roots to the leaves of a tree. Explain the following observations by referring to the properties of water: o Coastal areas have milder climates than adjacent inland areas. o Ocean temperatures fluctuate much less than temperatures on land. o Insects like water striders can walk on the surface of a pond without breaking the surface. Creative Commons Attribution 3.0 Unported License 6 BIOLOGY SEMESTER ONE COURSE OUTLINE o If you slightly overfill a water glass, the water will form a convex surface above the top of the glass. o If you place a paper towel so that it touches spilled water, the towel will draw in the water. o Ice floats on water. o Humans sweat and dogs pant to cool themselves on hot days. Understand molarity, and explain how you would make up a one molar (1M) solution of a solute. Explain how acids and bases may directly or indirectly alter the hydrogen ion concentration of a solution. Unit 4 Explain how carbon’s electron configuration explains its ability to form large, complex and diverse organic molecules. Describe the basic structure of a hydrocarbon and explain why these molecules are hydrophobic. Distinguish among the three types of isomers: structural, geometric, and enantiomer. Name the major chemical groups found in organic molecules. Describe the basic structure of each chemical group and outline the chemical properties of the organic molecules in which they occur. Explain how ATP functions as the primary energy transfer molecule in living cells. Unit 5 List the four major classes of macromolecules. Draw diagrams to illustrate condensation and hydrolysis reactions. Distinguish between monosaccharides, disaccharides, and polysaccharides. Describe the formation of a glycosidic linkage, and distinguish between the glycosidic linkages found in starch and cellulose. Explain why the difference is biologically important. Describe the building-block molecules, structure, and biological importance of fats, phospholipids, and steroids. Identify an ester linkage and describe how it is formed. Distinguish between saturated and unsaturated fats. Distinguish between cis and trans fat molecules. Name the principal energy storage molecules of plants and animals. List and describe the four major components of an amino acid. Explain how amino acids may be grouped according to the physical and chemical properties of the R group. Explain what determines protein structure and why it is important. Explain how weak interactions and disulfide bridges contribute to tertiary protein structure. List four conditions under which proteins may be denatured. List the major components of a nucleotide, and describe how these monomers are linked to form a nucleic acid. Briefly describe the three-dimensional structure of DNA Explain how DNA or protein comparisons may allow us to assess evolutionary relationships between species. Creative Commons Attribution 3.0 Unported License 7 BIOLOGY SEMESTER ONE COURSE OUTLINE Unit 6 Understand the principles of light microscopy, transmission electron microscopes, and scanning electron microscopes. Distinguish between prokaryotic and eukaryotic cells. Understand the upper and lower limits to cell size, and be able to explain the advantages of compartmentalization in eukaryotic cells. Briefly explain how the nucleus controls protein synthesis in the cytoplasm, and explain the role of the nucleolus, smooth and rough ER, the Golgi apparatus and ribosomes in protein synthesis. List the components of the endomembrane system, and describe the structure and function of each component. Understand means of intracellular digestion by lysosomes. Understand the roles of vacuoles. Be able to explain the energy conversions carried out by mitochondria and chloroplasts. Describe the structure of a mitochondrion and a chloroplast, and explain the functional importance of compartmentalization in these organelles. Describe the evidence that mitochondria and chloroplasts are semiautonomous organelles. Describe the structure and function of the various components of the cytoskeleton (e.g. microtubules, microfilaments, intermediate filaments, centrioles and basal bodies). Describe the basic structure of a plant cell wall. Describe the structure and roles of the extracellular matrix in animal cells, and explain how it may act to integrate changes inside and outside the cell. Name the intercellular junctions found in plant and animal cells and list the function of each type of junction. Unit 7 Explain how the fluid mosaic model of membrane structure explains experimental findings: o Actual membranes adhere more strongly to water than do artificial membranes composed only of phospholipids. o Membranes with different functions may differ in type and number of membrane proteins. o Membrane proteins are not very water-soluble. o EMs of freeze-fracture membrane preparations show protein particles interspersed in a smooth matrix. Explain how membrane fluidity is influenced by temperature and membrane composition, and explain how cholesterol resists changes in membrane fluidity as temperatures change. Understand the various functions of membrane proteins. Explain the role of membrane carbohydrates in cell-cell recognition. Define diffusion and understand why it is a passive and spontaneous process; compare with osmosis, facilitated diffusion, and active transport. Explain why a concentration gradient of a substance across a membrane represents potential energy. Describe how living cells with and without cell walls regulate water balance. Creative Commons Attribution 3.0 Unported License 8 BIOLOGY SEMESTER ONE COURSE OUTLINE Describe the two forces that combine to produce an electrochemical gradient. Explain how an electrogenic pump creates voltage across a membrane. Describe the process of cotransport. Explain how large molecules are transported across a cell membrane. Distinguish between exocytosis and receptor-mediated endocytosis. Unit 8 Explain the role of catabolic and anabolic pathways in cellular metabolism. Distinguish between kinetic and potential energy. Distinguish between an isolated and an open system. Explain why an organism is considered an open system. Explain the first and second laws of thermodynamics, and explain why highly ordered living organisms do not violate the second law of thermodynamics. Distinguish between exergonic and endergonic reactions in terms of free energy change. Explain why metabolic disequilibrium is one of the defining features of life. List the three main kinds of cellular work. Explain in general terms how cells obtain the energy to do cellular work. Describe the structure of ATP, and explain how ATP performs cellular work. Describe the function of enzymes in biological systems, and describe mechanisms by which enzymes lower activation energy. Explain how substrate concentration affects the rate of an enzyme-catalyzed reaction, and how temperature, pH, cofactors, and enzyme inhibitors can affect enzyme activity. Unit 9 Understand and distinguish between fermentation and cellular respiration. Define oxidation and reduction, and explain how redox reactions are involved in energy exchanges. In general terms, explain the role of the electron transport chain in cellular respiration. Identify the three stages of cellular respiration and state the region of the eukaryotic cell where each stage occurs. Understand the process of glycolysis, and explain why ATP is required for the preparatory steps of glycolysis. Identify where substrate-level phosphorylation and the reduction of NAD+ occur in glycolysis. Describe where pyruvate is oxidized to acetyl CoA, what molecules are produced, and how this process links glycolysis to the citric acid cycle. List the products of the citric acid cycle. Explain why it is called a cycle. In general terms, explain how the exergonic “slide” of electrons down the electron transport chain is coupled to the endergonic production of ATP by chemiosmosis. Explain where and how the respiratory electron transport chain creates a proton gradient. Explain why this gradient is described as a proton motive force. Distinguish between fermentation and anaerobic respiration, and understand their functions. Compare the processes of fermentation and cellular respiration. Creative Commons Attribution 3.0 Unported License 9 BIOLOGY SEMESTER ONE COURSE OUTLINE Describe the evidence that suggests that glycolysis is an ancient metabolic pathway. Explain how glycolysis and the citric acid cycle can contribute to anabolic pathways. Explain how ATP production is controlled by the cell. Unit 10 Distinguish between autotrophic and heterotrophic nutrition. Describe the structure of a chloroplast, listing all membranes and compartments. Write a summary equation for photosynthesis, and describe the two main stages of photosynthesis. In general terms, explain the role of redox reactions in photosynthesis. Describe the relationship between an action spectrum and an absorption spectrum. List the components of a photosystem and explain the function of each component. Trace the movement of electrons in linear electron flow. Trace the movement of electrons in cyclic electron flow. Explain the functions of each. Describe the similarities and differences in chemiosmosis between oxidative phosphorylation in mitochondria and photophosphorylation in chloroplasts. State the function of each of the three phases of the Calvin cycle. Describe the role of ATP and NADPH in the Calvin cycle. Describe the major consequences of photorespiration. Explain why it is thought to be an evolutionary relict. Describe photosynthetic adaptations that minimize photorespiration. Unit 11 Describe how associated membrane proteins can facilitate metabolic pathways. State and describe the two types of cell signaling that are used to pass information through the plasma membrane (without passing chemicals through the membrane). Relating to chemical signaling: o State the three steps of chemical signaling: reception, transduction, response. o Describe the relationship between signal molecules and cell surface receptors, and give examples of each. Describe G-protein-linked receptors and receptor tyrosine kinases, and explain the role of each in receiving chemical signals and initiating signal transduction pathways. Describe a signal transduction pathway and explain how this multi-step process can amplify the signal and lead to a cellular response. Give examples of cellular responses initiated by signal transduction pathways. Unit 12 Describe and compare the structural organization of the prokaryotic and eukaryotic genomes. Describe and name the sequence of phases of the cell cycle, identifying key events throughout interphase and mitosis. Creative Commons Attribution 3.0 Unported License 10 BIOLOGY SEMESTER ONE COURSE OUTLINE Describe the structure and functions of the mitotic spindle, including centrosomes, kinetochore microtubules, nonkinetochore microtubules, and asters. Compare cytokinesis in animals and plants. Discuss binary fission and explain how mitosis may have evolved from binary fission in bacteria. Describe key “checkpoints” in the cell cycle, and explain how the abnormal cell division of cancerous cells escapes normal cell cycle controls. Unit 13 Distinguish between the following terms: somatic cell and gamete; autosome and sex chromosomes; haploid and diploid. Describe the events that characterize each phase of meiosis. Compare and contrast meiosis and mitosis, including the ultimate purpose of each. Distinguish between asexual and sexual reproduction and outline the benefits of each. Describe alternation of generation in animals, plants and fungi. Unit 14 Understand and use the terminology related to Mendelian genetics. Identify and explain the four components of Mendel’s segregation model of genetic inheritance. Create and use Punnett squares to predict the outcomes of various crosses. Understand and apply the laws of probability (multiplication & addition rules) to Mendelian inheritance. Discuss Mendel’s laws of segregation and independent assortment and relate them to meiosis. Discuss various forms of genetic dominance (eg: complete / incomplete / codominant / recessive) and how they may apply to phenotype. Explain why dominant alleles are not necessarily more common in a population. Discuss gene interaction (eg: epistasis) and environmental influence on phenotype. Discuss how alleles arise and are maintained in populations, even when they appear to be non-beneficial or even harmful. Unit 15 Explain how the observations of cytologists and geneticists provided the basis for the chromosome theory of inheritance. Describe how sex is genetically determined in humans and in other types of organisms. Discuss inheritance patterns of sex-linked genes, and explain why certain diseases are more common in human males. Creative Commons Attribution 3.0 Unported License 11 BIOLOGY SEMESTER ONE COURSE OUTLINE Describe the process of X inactivation in female mammals. Explain how this phenomenon produces the tortoiseshell colouration in cats. Distinguish between linked, unlinked, and sex-linked genes. Describe the independent assortment of chromosomes during Meiosis I. Explain how independent assortment of chromosomes produces genetic recombination of unlinked genes, and explain why linked genes do not assort independently. Explain how crossing over can unlink genes. Explain how nondisjunction can lead to aneuploidy, and understand trisomy and polyploidy. Explain how these major chromosomal changes occur and describe possible consequences. Distinguish among deletions, duplications, inversions, and translocations, and discuss effects. Unit 16 Trace how major experiments and studies in molecular genetics have led to our current understanding of DNA. Describe the structure of DNA. Explain the base-pairing rule and describe its significance. Describe the semiconservative model of replication Describe the process of DNA replication, including the role of the origins of replication and replication forks, DNA polymerases, Okazaki fragments. Understand the roles of DNA polymerase, mismatch repair enzymes, and nuclease in DNA proofreading and repair. Describe the structure and function of telomeres, and explain the possible significance of telomerase in germ cells and cancerous cells. Understand the significance of, and describe the packing of chromatin changes throughout the cell cycle. Unit 17 Distinguish between the “one gene-one enzyme” hypothesis and the “one gene-one polypeptide” hypothesis and explain why the original hypothesis was changed. Explain how RNA differs from DNA. Briefly explain how information flows from gene to protein. Describe the events and locations associated with transcription and translation, and compare between eukaryotes and bacteria. Using a chart, be able to identify what amino acids are specified by various codons. Define and discuss redundancy and ambiguity in the genetic code. Explain the significance of the reading frame during translation. Explain the evolutionary significance of a nearly universal genetic code. Explain how RNA polymerase recognizes where transcription should begin. Describe the role of the promoter, the terminator, and the transcription unit. Describe the functional and evolutionary significance of introns. Explain why, due to alternative RNA splicing, the number of different protein products an organism can produce is much greater than its number of genes. Describe the significance of polyribosomes. Creative Commons Attribution 3.0 Unported License 12 BIOLOGY SEMESTER ONE COURSE OUTLINE Explain what determines the primary structure of a protein and describe how a polypeptide must be modified before it becomes fully functional. Define “point mutations”. Distinguish between base-pair substitutions and base-pair insertions. Give an example of each and note the significance of such changes. Distinguish between a mis-sense and a nonsense mutation. Unit 18 Briefly describe strategies that cells use to control metabolism. Explain the adaptive advantage of bacterial genes grouped into an operon. Explain how repressible and inducible operons differ and how those differences reflect differences in the pathways they control. Distinguish between positive and negative controls, and give examples of each. Discuss differential gene expression. Explain how DNA methylation and histone acetylation affects chromatin structure and the regulation of transcription. Discuss epigenetic inheritance. Define control elements and explain how they influence transcription. Explain the role of promoters, enhancers, activators, and repressors in transcriptional control. Describe the controls for gene expression from pre-transcription to post-translation. Distinguish between determination and differentiation. Explain why determination precedes differentiation. Explain how maternal effect genes affect polarity and development, using an example. Explain how mutations in tumour-suppressor and other genes can contribute to cancer. Unit 20 DNA Cloning Describe the natural function of restriction enzymes and explain how they are used in recombinant DNA technology. Explain how the creation of sticky ends by restriction enzymes is useful in producing a recombinant DNA molecule. Outline the procedures for cloning a eukaryotic gene in a bacterial plasmid. Explain the rationale for including a gene for antibiotic resistance and a gene that codes for a hydrolytic enzyme in the plasmid. Define and distinguish between genomic libraries using plasmids, phages, and cDNA. Describe the role of an expression vector. Describe two advantages of using yeast cells instead of bacteria as hosts for cloning or expressing eukaryotic genes. Describe the structure and function of a yeast artificial chromosome (YAC). Describe two techniques to introduce recombinant DNA into eukaryotic cells. Describe the polymerase chain reaction (PCR) and explain the advantages and limitations of this procedure. Creative Commons Attribution 3.0 Unported License 13 BIOLOGY SEMESTER ONE COURSE OUTLINE Using DNA Technology to Explore Gene Function Explain how gel electrophoresis is used to analyze nucleic acids and to distinguish between two alleles of a gene. Describe the process of nucleic acid hybridization. Describe the Southern blotting procedure and explain how it can be used to identify the heterozygous carriers of a mutant allele. Explain how Northern blotting or the reverse transcriptase-polymerase chain reaction (RTPCR) can be used to determine how expression of a gene changes at different stages of embryonic development. State two questions that could be addressed through genome-wide expression studies. Explain how in vitro mutagenesis and RNA interference help researchers to discover the functions of some genes. Organismal Cloning Distinguish between gene cloning, cell cloning, and organismal cloning. Explain why it is so much easier to clone plants than animals. Describe how nuclear transplantation was used to produce Dolly, the first cloned sheep. Explain why cloned animals are so likely to have defects. Distinguish between reproductive cloning and therapeutic cloning. Distinguish between embryonic and adult stem cells. Practical Applications of DNA Technology Describe how DNA technology has medical applications in the diagnosis of genetic disease, the development of gene therapy, vaccine production, and the development of pharmaceutical products. Explain how genetic markers can be used to detect abnormal alleles of a gene that has not yet been cloned. Define a single nucleotide polymorphism. Explain how an SNP may produce a restriction fragment length polymorphism (RFLP). Describe how gene therapy was used to treat severe combined immunodeficiency (SCID), with mixed success. Describe an example of a transgenic animal used as a pharmaceutical factory. Explain how DNA technology can be used to improve the nutritional value of crops and to develop plants that can produce pharmaceutical products. Explain how DNA technology is used in the forensic sciences. Describe how gene manipulation has practical applications in environmental cleanup and agriculture. Describe how plant genes can be manipulated using the Ti plasmid carried by Agrobacterium as a vector. Discuss the safety and ethical questions related to recombinant DNA studies and the biotechnology industry. Describe the current controversy over genetically modified (GM) foods. Creative Commons Attribution 3.0 Unported License 14 BIOLOGY SEMESTER ONE COURSE OUTLINE NANSLO Biology Core Units and Laboratory Experiments by the North American Network of Science Labs Online, a collaboration between WICHE, CCCS, and BCcampus is licensed under a Creative Commons Attribution 3.0 Unported License; based on a work at rwsl.nic.bc.ca. Funded by a grant from EDUCAUSE through the Next Generation Learning Challenges. Creative Commons Attribution 3.0 Unported License 15