番茄社区 - Biochemistry and Microbiology - Undergraduate - Course Outlines

Course Information

Please see the for a complete list of our programs and courses.

Course Outlines
Expected Learning Outcomes

Fall 2023 Course Outlines

BCMB 301A
BCMB 406A
BCMB 489
BIOC 300A
BIOC 402
BIOC 403
BIOC 404
BIOC 409
MICR 200A
MICR 303
MICR 402

Summer 2023 Course Outlines

BCMB 301A
BCMB 301B
BCMB 406A
BCMB 406B
BIOC 300A
BIOC 300B

Summer 2015 course outlines

BCMB 301A
BCMB 301B
BIOC 300A
BIOC 300B
MICR 302

Expected learning outcomes

Below you will find the expected learning outcomes for our programs and for each of our undergraduate courses.

What will I learn in Biochemistry and Microbiology?

All students graduating from the programs offered by the Department of Biochemistry and Microbiology will have a solid grounding in basic science theory: Mathematics/Statistics; Physics; Molecular and Cellular Biology; Chemistry.

In addition:

1) All students should understand the basics of:
BIOCHEMISTRY
• the structure and function of DNA, RNA, proteins, lipids and carbohydrates
• the principles of enzymes and enzyme kinetics
• bioenergetics
• metabolic processes and their control
• gene structure and regulation

MICROBIOLOGY and IMMUNOLOGY
• prokaryotic and eukaryotic cell structure and function
• prokaryotic physiology, growth and taxonomy
• the principles of microbial genetics and genomics
• principles of immunology: generation of antibody diversity, immune effector mechanisms
• molecular techniques and their application in biotechnology

2) All students should have further in-depth knowledge of several areas related to their chosen discipline: gene expression, epigenetics, signal transduction, proteins, biotechnology, microbial pathogenesis, virology, cell biology, genomics, organic chemistry.

3) All students will have experience in microbiology and biochemistry laboratory techniques including: following protocols, data collection and evaluation, troubleshooting, write-up and presentation of results. Co-op and Honours students will also have more extensive experience and worked on hypothesis development and experimental design.

4) All students will have a range of computer skills including: literature search strategies and literature management tools, use of word-processing, spreadsheet and presentation tools, use of internet-based tools for basic DNA and protein analysis.

BCMB 301 A/B

BCMB 301A & 301B Lab Techniques and Projects I & II

These courses are open to Biochemistry and Microbiology majors only. In order to register for these courses, you will need to first declare your program at .

In BCMB 301, students employ fundamental biochemical, microbiological and molecular biological laboratory techniques to investigate experimental problems. Using data generated in a range of experiments, students apply relevant theoretical concepts to analyse the data and evaluate experimental outcomes. In addition to developing analytical and practical laboratory skills, students develop problem solving and critical thinking skills by relating acquired knowledge to new problems or trouble-shooting questions. Students practice scientific writing by communicating their experimental findings in laboratory reports.

Upon successful completion of BCMB301 students are expected to: demonstrate competence in the laboratory techniques employed such as setting up assays, pouring and running gels, protein purification, molecular cloning techniques, and sterile technique in tissue culture experiments; perform calculations for solution preparation, serial dilutions, and analysing data; develop time management skills by organizing the experimental components in an efficient manner; demonstrate an understanding of principles studied by applying that understanding to new problems; communicate scientific principles effectively; and keep accurate records of their experimental work.

BCMB 406 A/B

BCMB 406 Applied Research Laboratory Techniques I & II

Utilizing current analytical techniques, students of BCMB 406 will explore contemporary topics in biochemistry, microbiology, immunology and molecular biology. Students will build upon the basic lab skills learned in BCMB 301 to complete complex assays in the laboratory while working both independently and cooperatively. Additionally, bioinformatics and in silico programs will be operated to analyse results and design experiments. Students will critically examine, troubleshoot, and interpret multiple sets of data to study complex problems and then parse their findings into well written scientific reports. During the course, a comprehensive written record of data will be maintained in the form of a laboratory journal.

Upon completion of BCMB 406, students are expected to be proficient in both the practical skills and in silico techniques learned. As well, students should be able to recognize, and explain the purpose of controls in scientific experimentation and then apply their understanding to problem solving and the design of novel experiments. Additionally, it is expected that they will be able to analyse scientific papers and use them to compare and interpret their experimental data.

BCMB 406A Specific Learning Objectives

Chromatin Immunoprecipitation (ChIP) Analysis along the YEF3 gene in S. cerevisiae

To understand and recognize the role of epigenetics in gene regulation
To utilize ChIP and QPCR to localize and quantitate the presence of two histone modifications along an active gene.

Using the experimental results obtained from a number of laboratory techniques (i.e. cell lysis, micrococcal nuclease digestion, cross linking, reverse cross-linking and DNA purification), students will be expected to explain the effect chromatin structure bears on the results. Additionally, students will be expected to be proficient in performing ChIP and interpreting ChIP experimental data. This interpretation will involve an in depth knowledge of controls, QPCR theory, and mathematical calculations related to QPCR analysis.

Immunological Characterization of Breast Cancer Cell Lines

To utilize flow cytometry, both adherent and suspension cell culture techniques, and a functional immunological assay to explain the specificity of the immune response (i.e. only tumour cells with a specific epitope can activate T cells) and the immune evasion strategies employed by tumours
To become familiar with the use of software (FlowJo) for analyzing flow cytometry data By the end of the lab, students will be expected to correlate phenotypic/immunological characteristics of a tumour cell line with a functional outcome (i.e. activation of T cells). Additionally, competency in basic tissue culture techniques including passaging adherent cell lines and the counting and diluting of cells is expected.

Isolation and Identification of Peptides and Proteins

To utilize MALDI-TOF mass spectrometry for m/z determination and identification of peptides separated by reverse phase high-performance liquid chromatography, and peptide mass fingerprinting (PMF) and tandem mass spectrometry (MS/MS) analysis of tryptic peptides derived from E. coli proteins following separation by 2D-PAGE.
To apply PMF and MS/MS data in the identification of proteins using online bioinformatics tools (specifically, MS-Fit and Mascot)

Students are expected to have a broad understanding of protein separation techniques, mass spectroscopy theory, ionization methods and their applications in the field of proteomics. Additionally, students will understand the significance of Mowse scores and percent coverage for protein identification using the bioinformatics tools.

BCMB 406B Specific Learning Objectives

Primer Design

Recognize the different PCR-based methods for performing site-directed mutagenesis
Design specific primers in silico for inverse PCR site-directed mutagenesis amplification Upon completion of this lab it is expected that students will be able to design and evaluate PCR primers using common web-based applications.

Site-Directed Mutagenesis of CBM Proteins

Utilize VectorNTI to design and troubleshoot an in silico experiment; using the data obtained, perform a site-directed mutagenesis using inverse PCR in the laboratory.
Evaluate the results obtained by restriction digestion and automated DNA sequencing in order to confirm the presence of the desired mutations using various bioinformatics tools Students are expected to be competent in inverse PCR, preparation of competent cells, electroporation & chemical transformation, purification of plasmids, and screening by restriction enzyme digestion and automated DNA sequencing after completion of this lab.

Mutant CBM Purification

To recognize the importance of studying mutant proteins
To design and implement a protein concentration assay
To utilize techniques and lab equipment associated with large-scale protein purifications, particularly nickel column purification techniques.

Introduction to crystallization using the hanging drop method

At the end of the lab, students should be competent growing and harvesting a large culture followed by a his-tagged protein purification from this culture. Students will be expected to understand how carbohydrate binding modules function within a glycoside hydrolase and how to apply the various techniques (macroarray and affinity gels) learned in this lab to compare the functioning of a mutant CBM protein to wild type protein.

BIOC 102

BIOC 102 Biochemistry and Human Health

BIOC 102 is an introduction to contemporary issues in human health that are relevant to everyone - not just scientists. There are no university science prerequisites for this course, and it is not open to students enrolled in, or with credit in, upper level science courses.

Molecular biology and genomics
Students who successfully complete this course will be able to: (1) demonstrate an understanding of basic molecular biology of cells and viruses; (2) describe and compare the general structures and functions of prokaryotic and eukaryotic genomes; (3) discuss recent advances in our understanding of gene regulation in the human genome; and (4) critically discuss the use of model organisms to study biochemical processes.

The promise of genomic medicine
Students who successfully complete this course will be able to outline the general goals of genomic medicine and to summarize its current status.

Using specific examples, they will be able to: (1) describe modern approaches to identify genes involved in human disease; (2) discuss general strategies for determining the biochemical basis for a human disease and for developing an intervention, e.g., a drug, to treat that disease; (3) describe the process involved in the development of molecular diagnostics for human diseases; and (4) describe how certain genetic diseases have been cured through gene therapy.

Immunology and Infectious diseases
Students who successfully complete this course will be able to describe the human immune system and (1) its roles in humoral and cell-mediated immunity, and (2) its involvement in the allergic and inflammatory responses.

They will be able to (1) assess the changes in the impact of infectious diseases on global public health in the past century; and (2) describe the continuing contributions of the Human Microbiome Project in our understanding of the roles of our resident microorganisms in health and disease.

Priorities, challenges, and recent breakthroughs
Students who successfully complete this course will be able to: (1) describe and apply selected modern research tools, e.g., DNA microarrays; (2) describe the goals of the Cancer Genome Atlas project and its influence on the current directions in cancer research; (3) critically discuss genetic engineering and genetically modified organisms, particularly as food; (4) describe and critically discuss animal cloning; (5) discuss the current status of therapeutic stem cell technology; and (6) discuss our current understanding of the human aging process and age-related diseases.

BIOC 299

BIOC 299 Biochemistry for Non-Majors

Students will obtain a comprehensive overview of the major concepts and principles of biochemistry through lecture presentations, assigned questions, and tests. Students will be able to define and describe the properties, and metabolism of the major classes of biomolecules: DNA, RNA, protein, carbohydrates, and lipids. Specific learning outcomes include:

Structure-function relationships of biomolecules. Through a variety of examples, students will be able to relate the chemical structures of biomolecules to their biological functions and demonstrate how they interact to accomplish fundamental metabolic processes.

Metabolism and regulation of biomolecules. For each class of molecule, students should be able to describe the fundamentals of biomolecule synthesis and breakdown, the role of biomolecule interactions, how a cellular signal is transduced to a biological outcome, and how gene expression accomplished through specific examples. A demonstrated knowledge of how biochemical pathways are controlled is also expected.

Experimental biochemistry and disease. Students should be familiar with basic experimental concepts and approaches used in biochemistry with classic experiments used as examples. Students should be able to identify the consequences of a variety of metabolic and genetic diseases and indicate what insight these diseases give on biochemical pathway function.

BIOC 300A

BIOC 300A General Biochemistry I

Bioc 300A is an introductory course covering the basic structural and functional characteristics of proteins, carbohydrates and lipids. By studying how the building blocks of these biological macromolecules are assembled into large polymers, students will gain an in-depth understanding of how structure relates to function in the biological world. Students will expected to apply their knowledge of the structure-function relationship to investigate various biological processes including how enzymes function and the corresponding mechanisms of inhibition.

BIOC 300B

BIOC 300B General Biochemistry II

BIOC 300B will examine the mechanisms and regulation of gene expression, from maintenance and replication of DNA to the production of gene products. Students will be able to identify themes and principles common to the processes of replication, transcription and translation. A particular focus of this course is to combine knowledge of biochemical processes with an understanding of how that knowledge can be applied in problem solving. Students should be able to apply their understanding of the principles related to these processes to solve problems in which these principles may be presented out of context. Students will also be able to apply their understanding of these processes and principles to evaluate experimental data and arrive at the solution to a posed problem.

Processes and regulation of major metabolic pathways for carbohydrates, lipids and amino acids will be presented. By the end of the course, students will be able to analyze the influence of individual pathways on overall metabolism of a cell. Additionally, students will be expected to predict cause and effect when metabolic processes are disrupted, especially as it applies to health of an organism.

BIOC 401

BIOC 401 Gene Expression in Eukaryotes

In BIOC 401 equal emphasis is placed on learning the principles of eukaryotic gene expression and developing analysis, communication and collaboration skills. There are three main elements to this course. Lectures are structured to introduce students to key concepts in gene, genome and RNA biology. There is a focus on recent scientific and technological advances that shape the current state of the field. The contributions of diverse scientists in RNA biology are highlighted. Throughout the course, the links between gene regulation processes and development/disease states is kept front-of-mind. Group discussions are focussed on breakthrough papers. They provide an opportunity to apply lecture knowledge, to practice peer-to-peer teaching/learning and analytical skills, and to observe how research evolves with new methods and technologies. A final independent project will allow each student to investigate and summarize cutting-edge research in gene regulation in an area of their choice. This exercise will allow students to apply concise and clear communication skills.

By the end of this course students will be able to:

Demonstrate a clear understanding of how the processes of transcription, RNA processing, mRNA nuclear export, mRNA sequestration, and translation are executed in eukaryotes. Students will be able identify recurring themes in regulatory principles across these topics.
Provide examples of how the processes of transcription, RNA processing, mRNA nuclear export, mRNA sequestration, and translation are coupled.
Apply the knowledge gained in lectures and in group discussions to problem solving, experimental design questions, and critical evaluation of literature.
Provide examples of how failure to execute regulation of genes leads to developmental failure or disease. Explain the biological/clinical relevance and significance of recent findings in the field of eukaryotic gene regulation
Critically evaluate, analyze and summarize primary literature. Students will be able to identify the key experiments and evidence provided in research papers.

BIOC 403

BIOC 403 Biochemistry of Signal Transduction

Diversity of signaling pathways: students should be able to recognize emerging patterns of pathway organization and give examples. They should be able to identify similarity and differences between pathways and apply their knowledge to novel problems.

How we study cellular signaling: students should be able to articulate how different types of experiments are performed and what information is gained from different experiments. It is expected that students will be able to apply this knowledge to novel biochemical problems.

Experimental basis for pathway summaries: students are expected to be able to describe how we know given information about a pathway. For example, what is the experimental evidence supporting a given claim?

Modularity of molecular components of signaling pathways: students are expected to be able to identify and describe the function of the major domains discussed in class. They should have an appreciation for why proteins are organized into domains, and how this type of organization facilitates the evolution of multicellular organisms.

Regulation of pathway components: students are expected to be able to identify and describe the biochemical mechanisms of how pathways are turned on and off including allosteric mechanisms. They should be able to appreciate the type of information gathered from structural approaches and how genetic and molecular approaches are used to test molecular models. They should be able to apply this information to novel problems.

Fidelity and specificity of signaling: students should be able to describe mechanisms of how the cell achieves specificity in signaling pathways. Using examples they should be able to describe the role of compartmentalization and scaffolds in limiting and amplifying signalling pathways. They should appreciate that pathways are interconnected and form networks. A basic understanding of how network regulation is studied is expected.

Critical Thinking: students should be able to interpret and critically review primary literature in the field. They will demonstrate this ability through assignments and exams. Student should be able to identify the hypothesis or questions being addressed in a journal article, determine whether the appropriate experiments and controls have been applied, and describe the strengths and weakness of the article.

BIOC 404

BIOC 404 Proteins

At the end of this course, students should be able to:

Apply thermodynamic and kinetic principles to rationalize how proteins adopt secondary, tertiary and quaternary structures.
Compare various protein purification strategies, and evaluate the strengths of different methods. Using this knowledge, students will be capable of designing a purification strategy for a model protein purification.
Explain the mathematical and biophysical techniques used to explore processes underlying protein structural analysis. Students will be capable of predicting how the physical state of a macromolecule will influence the likelihood that its structure can be determined using major biophysical techniques.
Apply knowledge of macromolecular structure to elucidate fundamental mechanisms of function, including protein-ligand interactions. Students will examine this concept as it applies to protein ubiquitination and G-protein signalling.
Describe how the instrumentation used in the major biophysical techniques records various phenomena to allow for insight into macromolecular folding, structure and/or function.
Outline the important steps in the determination of macromolecular structure by x-ray crystallography and/or nuclear magnetic resonance, and describe how such knowledge can be used to critically evaluate scientific publications that utilize these major biophysical techniques.

Overall, this course will provide students with the fundamental skills to analyze proteins at a molecular level. These skills will be applied to designing protocols for purifying proteins and examining their interactions with other proteins and substrates, as well as evaluating or elucidating enzyme mechanism. This knowledge will also translate to the ability to critically evaluate peer-reviewed literature in the area of protein research.

BIOC 408

BIOC 408 Chromatin & Epigenetics

This course combines two complimentary views on genome regulation; the structural and functional properties of chromatin are interrogated from a biochemical/biophysical perspective, while research using a diversity of model organisms is used to demonstrate the contributions of epigenetics to organism development, behavior and disease. The course is heavily focused on primary research papers. Besides the formal lectures, the course consists of regular group discussion sessions, and capstone student presentations that take the form of mini-lectures.

•    Formal lectures introduce essential background material, and key concepts. Throughout the course, there is a strong emphasis on the understanding of experimental methods and their application to test hypotheses.

•    Discussion Groups are centered on readings of companion research papers.These articles provide an opportunity to apply lecture knowledge, to practice peer-to-peer teaching, and to witness how methods are applied in research.

•    Capstone group presentations allow the students to play an active role in determining course content. These presentations take place at the end of the course, when student groups summarize a recent advance, new topic or paradigm shift in chromatin and epigenetics. It is expected that material from 1-3 recent research papers will be the basis of the lecture.

By the end of this course students will be able to:

1. Recognize the importance of epigenetic mechanisms in the regulation of genes, development and behaviour, and explain the role of epigenetics in Nature and Nurture.

2. Identify the fundamental elements of euchromatin and heterochromatin and distinguish between different molecular mechanisms that establish and reinforce these epigenetic states.

3. Explain how chemical and social factors in the environment can affect the compositional characteristics of chromatin and alter epigenomes and behavior. Students will be able to recognize why some diseases are amenable to treatments that can reverse the altered epigenomic state.

4. Describe how different model organisms can be used to identify and understand epigenetic mechanisms of genome regulation.

5. Apply the knowledge gained in lectures and in group discussions, to problem solving, experimental design questions, and critical evaluation of literature.

6. Explain the biological relevance and significance of recent findings in the field of chromatin and epigenetics and identify the key experiments in research papers.

BIOC 409

BIOC 409 Proteomics

This course is an introduction to the science of proteomics, which concerns the study of proteins. The expected learning outcomes reflect what is expected after a general survey of the primary technology used for protein analysis (mass spectrometry) and its role (along with ancillary technologies) in biomedical research and in health and disease.

Introduction to mass spectrometry for biological applications.
Students will be expected to learn about mass spectrometry systems architecture and analytical strategies for the detection, characterization and quantitation of proteins and the identification and localization of protein post-translational modifications. Students must learn some problem-solving strategies and be able to interpret several kinds of mass-spec data.

Use of antibodies coupled with mass spectrometry to measure proteins in complex biological systems.
Students are expected to learn about the use of antibodies for sample enrichment applied to both top-down and bottom-up immuno-MS methods for protein quantitation. Students are expected to understand the use of immuno-MS in biomarker validation and clinical assay development.

Use of proteomics methods for studying biological research problems.
Students will be expected to learn how to study protein-protein interactions using biochemical-mass spectrometry strategies, to investigate bacterial pathogenesis and to study ion channel signaling networks and dynamic biological systems.

In summary, the expected learning outcomes are based on understanding how mass spectrometry and associated technologies are used to study proteins both qualitatively and quantitatively. This will allow students to make informed decisions regarding proteomics approaches to biological and clinical research problems.

MICR 200A

MICR 200A Introductory Microbiology I

Students will gain insight into historical events that initially identified microbes. Processes used to establish the role of microbes in important processes such as disease will also be examined and students will be able to compare these methods to modern techniques utilized in the field of microbiology.
The major structural components of bacteria, archae and eukaryotes will be described. Utilizing this information, students will be able to compare the structures between these organisms, and rationalize why they have evolved specific adaptations.
Conditions for growth of microbes, both in natural and laboratory settings will be examined. Students will demonstrate the ability to apply this knowledge to both identify and classify microbes. Additionally, students will learn to categorize microbes based on a variety of phenotypic and genotypic traits.
Metabolic pathways will be described in the context of microbes, and compared to more complex systems, particularly humans. The suitability of using bacteria as a model organism for higher order eukaryotic organisms will be appraised.
Students should be able to describe the basics of virion structure, virus replication, viral gene regulation and the difficulties of making anti-viral drugs and vaccines for example viruses such as polio, flu, HIV and phage.
The laboratory component of the course provides students with independent hands-on learning opportunities in basic microbiology techniques, such as aseptic technique, light microscopy, techniques for isolation and enumeration of bacteria, use of general purpose, selective and differential growth media, in addition to characterizing and identifying bacteria at the cellular level or based on phenotypic display on growth media. This approach serves to develop student confidence in the lab and generate an awareness of how to work safely in a biosafety level 2 facility. All labs provide "context narratives" in that lab exercises are linked to a story or particular "problem" that the student must solve; the lab also brings specific theory components from the lecture into the practical lab, which provides a bridge for students to in their understanding of course material and starts to develop their critical thinking skills. The lab also provides students with an introduction to environmental microbiology and clinical microbiology, and the molecular techniques of plasmid DNA isolation and agarose gel electrophoresis.

MICR 200B

MICR 200B Introductory Microbiology II

The genetics of microbes will be introduced. Students will recognize the importance that genetic processes play in both health and industry.

Interactions between microbes and the environment will be described. Students will be expected to apply their knowledge of genetics, as well as biochemical pathways (from MICR200A) to analyze how microbes not only survive in a particular environment, but how they actually shape their physical environment. Students will evaluate how environmental manipulation by microbes impacts ecosystems. This theme will be carried into humans as a microbial environment. Students will recognize both beneficial and harmful (pathogenic) interactions between human hosts and microbes. Strategies to protect humans from disease will be described. Students will be expected to appraise different strategies to protect and promote human health.

The immunology portion of the course is a first introduction to the science of immunology thus the expected learning outcomes reflect what is expected after a very short introduction of the immune system and its role in health and disease.

Students are expected to learn about the origin and genesis of the cells involved in immunity, their function, their role in the immune organs and their organization into the lymphatic system.
Students are expected to understand the basis of recognition of dangerous vs nondangerous molecules and cells ("danger theory" of immune recognition).
Students are expected to understand both antibody-mediated and cell-mediated immune responses and their role in autoimmunity, immunodeficiency disorders, cancer, transplantations and pregnancy in order that they can follow the field of immunology in their future lives and make health decisions based on their understanding.

The lab component of the course provides students with hands-on learning opportunities in basic microbiology techniques, revisiting and building on some of the techniques from Microbiology 200A in addition to introducing techniques in molecular biology, such as PCR. Students will continue to develop confidence and independence while working in a biosafety level 2 lab facility. All labs provide "context narratives" in that lab exercises are linked to a story or particular "problem" that the student must solve; the lab also brings specific theory components from the lecture into the practical lab, which provides a bridge for students to in their understanding of course material and starts to develop their critical thinking skills. The lab also provides students with an introduction to topics and techniques specific to virology, food safety, clinical microbiology and serology.

MICR 302

MICR 302 Molecular Microbiology

In this course, you will gain the tools to recognize relationships between DNA, RNA and protein. Applying these tools, you will be able to evaluate the specific contributions of different molecular mechanisms microbes utilize to respond to environmental changes.
You will have the ability to compare microbial communication and signalling strategies.

By the end of the course, it is expected that each student will be capable of examining a biological response and hypothesizing which underlying genetic and/or biochemical process defines the response. Students will then be able to design experiments, including all relevant controls, to test their proposed hypothesis.

MICR 303

MICR 303 Immunology

This course is a first introduction to the science of immunology thus the expected learning outcomes reflect what is expected after a general survey of the immune system and its role in biomedical research and in health and disease.

Components of the immune system and how they function to generate diversity in immune responses. Students are expected to learn about the genesis of the cells involved in immunity, their function, their role in the immune organs and their organization into the lymphatic system. An understanding of the molecular characteristics of immunogens (molecules that induce immune responses), the molecular basis of the generation of antibody diversity and the structure-function relationships of antibody-antigen interactions will also be expected.
Antibody-mediated and cell-mediated immune responses and antigen recognition. Students are expected to understand the molecular and cellular basis of recognition of dangerous vs non-dangerous molecules and cells (“danger theory” of immune recognition). An understanding of how antibody-mediated and cell-mediated wings of the immune system interact to regulate the immune response is also an expected learning outcome. How immune balance is maintained in health and altered in disease states must be understood to allow immunological thinking about the clinical aspects of immunology presented in the last third of the course.
The immune system and its functional role in health and disease. Students are expected to understand the roles played by antigen presenting cells, lymphocytes cytokines, and cell-cell interactions in regulating immune responses in tolerance and autoimmunity, immunodeficiency disorders, cancer, transplantations and pregnancy in order that they can follow the field of immunology in their future lives and make health decisions based on their understanding.

In summary, the expected learning outcomes are based on studying molecular and cellular mechanisms involved in maintenance of an individual’s biological integrity through interest and excitement rather than from fear, setting information in a larger context in order to stimulate imagination.

MICR 402

MICR 402 Virology

History of Virology: Students should understand the methodologies of the key events in the history of this science and appreciate how they relate to the current knowledge at that time.

Virus Structure: Students are expected to be able to critically compare the key structural features of icosahedral, helical and complex viruses, with examples of each.

Virus Replication and Genomics: Students should understand the general processes by which different viruses evolve and the consequences of these processes. They should be able to describe the structure of viral genes, the relationship between ORFs and genes and how these are characterized and identified using bioinformatics.

Consequences of Virus Infection: Students are expected to be able to describe how viruses interact with their hosts, at the cellular and organismal levels and how virus genes control these events.

Viruses and the Immune System: Students should be able to explain those aspects of the immune system that involve resistance to viruses and the fight against virus infections.

Viral Pathogenicity: Students should be able to explain virus virulence and it relates to disease and host defenses.

Viral Vaccines: Students should be able to discuss the various methods of vaccine function and the implications of vaccination and problems of vaccine implementation in the population.

Virus Families: For the following types of viruses, student should be able todescribe the viral structure, genome structure and processes of replication, transcription and protein level control:

+ve sense RNA genomes: e.g. Polio, TMV, MS2, Rubella virus, SARS
-ve ssRNA genomes: e.g. Rabies virus, flu virus
dsRNA genomes: e.g. Reoviruses, rotavirus
Retroviruses: e.g. ALV, HTLV, SIV, HIV
Small DNA genomes: e.g. Parvoviruses, papillomaviruses
Large DNA genomes: e.g. Poxviruses, herpesviruses

More in depth knowledge of polio, flu, HIV, vaccinia and TMV will be expected as these used as examples for many discussions during the course.

MICR 405

MICR 405 Biotechnology, Proteomics and Synthetic Biology

After taking this course the student will:

Understand the strategies used for molecular cloning, DNA sequencing, genome modification, and DNA fragment assembly.
Have a sense of the workflow in biotechnology from discovery of a new biologic product, optimization of its function, and development of an appropriate downstream processing method.
Know how to apply biotechnology and synthetic biology tools to solve biomedical, industrial and environmental problems.

MICR 408

MICR 408 Microbial Pathogenesis

Host defense mechanisms and bacterial avoidance mechanisms:

Students are expected to understand and describe the major defense mechanisms employed by the host to combat bacterial pathogens, and the main mechanisms used by bacterial pathogens to circumvent these host defense mechanisms.

Key strategies used by bacteria to initiate and maintain infection:

Students are expected to understand and describe the main pathogenic mechanisms used by bacteria to cause infection. Examples include:

What are the types of secretion systems used by bacteria, how do they work and how do they facilitate infection of a host?
What are the strategies used by bacterial pathogens for intracellular and tissue invasion, and how are these two concepts different?
Can you predict infection "success" by assessing a pathogen's ability to adhere to a host surface?

Selected mechanisms of bacterial pathogenesis:

Students will be able to understand and describe the classic mechanisms that bacteria use to cause infection, and recognize how these mechanisms are interrelated and facilitate a robust bacterial infection.

Pathogenesis of selected organisms:

Students will be able to identify and explain the major mechanisms of pathogenesis for a variety of significant and medically relevant bacterial pathogens. What distinguishes these bacterial pathogens from others? What similar pathogenic themes are utilized by different bacterial pathogens?

Mechanisms of interference with pathogenesis:

Students will be able to understand and explain the primary mechanisms of action for prominent antibiotic classes and novel antibacterial compounds that are entering the pharmaceutical/biotechnology pipeline. Students will be able to understand and explain how antibiotic resistance arises within bacteria, and identify which bacterial pathogens are particularly adept at developing resistance to antibiotics and distinguish why this resistance arises so easily in these pathogens.

Techniques for studying pathogenesis:

Students will be able to identify and explain experimental techniques for addressing pertinent questions surrounding bacterial pathogenesis, including cutting edge approaches such as proteomics and systems biology. Students will be able to predict the “best” experimental technique to use for answering critical experimental questions.

Critical thinking:

Students are expected to be able to critique current, relevant primary literature papers that focus upon the most pertinent subjects surrounding bacterial pathogenesis. Students will be able to identify the critical questions being asked in the assigned primary literature papers, interpret how these questions further the field of research, and predict essential future questions that will significantly advance the scientific discipline.