Download Biology: semester one: course outline

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:
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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'
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BIOLOGY SEMESTER ONE
COURSE OUTLINE
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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
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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:
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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
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BIOLOGY SEMESTER ONE
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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
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Chapters 3, 4 & 5
Chapters 6 & 7
Chapters 8 & 9
Chapter 10
Chapters 14 & 15
Chapters 15 & 16
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Week 14
Week 15
Week 16
From Gene to Protein (cont’d)
Regulation of Gene Expression
Biotechnology
Exam Review
Final Exam
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Chapters 17 & 18
Chapter 20
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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
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BIOLOGY SEMESTER ONE
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APPENDIX A: DETAILED LEARNING OBJECTIVES
Unit 1
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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
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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
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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.
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BIOLOGY SEMESTER ONE
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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
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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
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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.
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Unit 6
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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
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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.
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BIOLOGY SEMESTER ONE
COURSE OUTLINE
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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
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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
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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.
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BIOLOGY SEMESTER ONE
COURSE OUTLINE
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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
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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
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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
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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.
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BIOLOGY SEMESTER ONE
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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
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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
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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
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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.
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BIOLOGY SEMESTER ONE
COURSE OUTLINE
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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
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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
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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.
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BIOLOGY SEMESTER ONE
COURSE OUTLINE
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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
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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
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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.
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BIOLOGY SEMESTER ONE
COURSE OUTLINE
Using DNA Technology to Explore Gene Function
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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
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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
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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.
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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.
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