Faculty of Arts & Science 2011-2012 Calendar

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Biochemistry

Faculty

Biochemistry is the study of the chemistry of living organisms. Biochemists seek a molecular explanation of life by attempting to understand its underlying principles. Biochemistry is concerned with the relevance of a molecule to an organism and the correlations between its structure and its function. Modern biochemistry grew out of the application of chemical techniques to biological problems and is the foundation of biological science and medicine. In many ways it combines biology and chemistry but the subject now covers such a broad range of activity that it is difficult to draw a neat border around biochemistry. Some of the most exciting areas of current biochemistry research include:

• structural biology
• enzyme mechanisms
• signal transduction and regulation
• biotechnology
• molecular cell biology
• gene expression and development
• metabolic diseases
• proteomics and bioinformatics
• molecular evolution
• protein folding
• membranes and transport

The Biochemistry Specialist Program is academically oriented and designed to provide students with a fundamental understanding of the theoretical and practical aspects of the discipline. The program offers training in problem solving specifically using a molecular approach. Biochemistry specialists will gain experience in critical thinking and the skills required to evaluate scientific rationale. The Biochemistry Major Program offers students fundamental training in the science and gives each student in the program the chance to combine Biochemistry with another relevant Major Program. This may be within the Life Sciences or Basic Sciences, or may be within the arts. For example, the combination of Biochemistry with Economics or with English could provide students with training relevant to the fields of investment within biotechnology or scientific journalism. Students who excel within the Biochemistry Major Program may be offered the chance to enter the Specialist Program at the third year. Frequently students who have completed a B.Sc. in the Specialist Program continue their studies in graduate programs in Biochemistry and other Life Sciences. Graduates from either the Specialist or Major Programs may find employment in research and teaching. Employers include universities and colleges, government laboratories, clinical biochemistry laboratories, forensic laboratories, pharmaceutical companies, biotechnology companies, and many other industries. Skills learned in the Biochemistry Specialist and Major Programs are also helpful in other areas such as marketing, finance, and law. Some biochemistry graduates continue their studies in medicine, dentistry or other health related programs.

Students considering choosing either the BCH Specialist or BCH Major program are encouraged to attend program information sessions to be held by the department in February and March. Please note that the Specialist program is the accepted route to graduate studies in Biochemistry and to careers in research.

Undergraduate Coordinator Dr. R. R. Baker, roy.baker@utoronto.ca

Undergraduate Administrator Jennifer Haughton, jennifer.haughton@utoronto.ca

Enquiries: Medical Sciences Building, Room 5207 (416-978-2700)

Web site: www.biochemistry.utoronto.ca

Biochemistry Programs

This is a limited enrolment subject POSt that can only accommodate a limited number of students.  Eligibility will be competitive and based on a student’s marks in the 3.0 required first-year courses:

BIO120H1, BIO130H1, (CHM138H1, CHM139H1)/CHM151Y1, and 1.0 FCE from (MAT135H1, MAT136H1)/MAT135Y1/MAT137Y1/MAT157Y1/(PHY131H1, PHY132H1)/(PHY151H1, PHY152H1) with an average of at least 70% on these 3.0 full-course equivalents (FCEs) and a final mark of at least 60% in each course.

While it is difficult to predict what will be competitive course marks and average in a given year,  based on previous years, the estimate is: course marks =  mid 80s; average = mid 80s.

Achieving these estimated marks does not guarantee admission to the subject POSt in any given year.

Note:  Students must apply to this program on the Arts & Science Faculty Registrar’s Office website (see the Registration Handbook & Timetable for instructions).

See the departmental web site at www.biochemistry.utoronto.ca for more information.

(14 full courses or their equivalent, including at least three 400 series courses)

First Year: BIO150Y1/(BIO120H1, BIO130H1); CHM151Y1/ (CHM138H1, CHM139H1); MAT135Y1/136Y1/MAT137Y1/(MAT135H1, MAT136H1); (PHY131H1, PHY132H1)/(PHY151H1,PHY152H1)/110Y1/138Y1/140Y1 [PHY131H1, PHY132H1 recommended]

Second Year:
1. BCH242Y1; BIO230H1/(BIO240H1, BIO241H1)/ BIO250Y1; CHM220H1*, CHM247H1/CHM249H1
2. One of: BIO260H1/HMB265H1/CHM221H1*

Third Year: BCH340H1, BCH371H1; MGY311Y1

Fourth Year:
1. BCH471Y1
2. Four half courses from the following list, including at least two BCH courses: BCH422H1/BCH425H1/BCH426H1/BCH440H1/BCH441H1/BCH444H1/BCH445H1/ BCH446H1/BCH447H1/BCH448H1/BCH479H1/BCB420H1/CHM447H1/MGY420H1/MGY425H1/MGY428H1/MGY451H1/MGY452H1/MGY470H1
BCH372Y1/BCH373H1/BCH375H1/BCH472Y1/BCH473Y1: One full credit from these optional research project courses may be taken for the Specialist program**.

Note: Some of the MGY courses noted above have BIO260H1 as prerequisite.

Over the course of the Specialist program, additional credits (to bring the program total to 14 full courses or their equivalent) from the following list: BIO220H1/BIO260H1/CHM217H1 (Analytical Chemistry)/CHM221H1* (Physical Chemistry II)/CHM225Y1 (Physical Chemistry)/CHM326H1 (Quantum Mechanics, Spectroscopy)/CHM328H1 (Physical Chemistry) /CHM342H1 (Organic Synthesis)/CHM347H1 (Organic Chemistry of Biological Compounds)/CSC108H1/CSC148H1/CSC150H1 (Introductory Computer Science, only one CSC course can be chosen)/HMB265H1/MAT235Y1/MAT237Y1 (Calculus II)/STA220H1/STA221H1/ any suitable 300-level course from CHM/CSB/EEB/HMB/IMM/LMP/MGY/PCL/PSL (departmental approval required)

*In lieu of CHM220H1 + CHM221H1, CHM225Y1 is an acceptable alternate credit for the Specialist program. CHM225Y1 and CHM221H1 have MAT235Y1/MAT237Y1 (Calculus II) as corequisite.

** Additional BCH research project courses can be taken as part of the 20 full credits needed for your degree, but if you take more than one full credit project course each must be taken with a different research supervisor.

This is a limited enrolment subject POSt that can only accommodate a limited number of students.  Eligibility will be competitive and based on a student’s marks in the 3.0 required first-year courses:

BIO120H1, BIO130H1, (CHM138H1, CHM139H1)/CHM151Y1, and 1.0 FCE from (MAT135H1, MAT136H1)/MAT135Y1/MAT137Y1/MAT157Y1/(PHY131H1, PHY132H1)/(PHY151H1, PHY152H1) with an average of at least 70% on these 3.0 full-course equivalents (FCEs) and a final mark of at least 60% in each course.

While it is difficult to predict what will be competitive course marks and average in a given year,  based on previous years, the estimate is: course marks =   high 70s; average =  high 70s.

Achieving these estimated marks does not guarantee admission to the subject POSt in any given year.

Note:  Students must apply to this program on the Arts & Science Faculty Registrar’s Office website (see the Registration Handbook & Timetable for instructions).

For more information, refer to the Biochemistry web site at www.biochemistry.utoronto.ca.

 NOTE  Students CANNOT combine a Biochemistry Major with a Cell & Molecular Biology Major.

8 full courses or their equivalent, including two 400-series half-year courses as noted below.

First Year: BIO150Y1/(BIO120H1, BIO130H1); CHM151Y1/ (CHM138H1, CHM139H1); MAT135Y1/136Y1/MAT137Y1/(MAT135H1, MAT 136H1)

Second Year: BCH210H1;BIO230H1/(BIO240H1, BIO241H1)/BIO250Y1; CHM247H1/CHM249H1

Third Year:
1. BCH370H1
2. BCH311H1
3. 1.5 full-course equivalents from the following list: BIO220H1/BIO260H1/CHM217H1/CHM220H1/HMB265H1/BCH340H1/ANY 300-level course(s) in CHM/CSB/EEB/HMB/IMM/LMP/MGY/PCL/PSL (departmental approval required) Students who have completed BCH304H1 may use the credit to partially fulfill this requirement.

Fourth Year: Two of: BCH422H1/BCH425H1/BCH426H1/BCH440H1/ BCH441H1/BCH444H1/BCH445H1/BCH446H1/BCH447H1/BCH448H1/CHM447H1

The Bioinformatics and Computational Biology Program is currently undergoing curriculum changes.  The Specialist Program will be outlined at the following website:  biochemistry.utoronto.ca/bcb. Following is the 2010-2011 version of the program requirements.

In principle, life is an expression of pure information, encoded in physical molecules. The more we discover about the details, the more we find that molecular biology is an information science as much as it is a physical science. Genome sequencing, proteome analysis and the study of cellular “systems” have given us breathtaking insights into the inner workings of biological function at the molecular level. However, a deep understanding of the complex organization of the cell and the interaction of its components has yet to be achieved. Substantial further progress will be needed to make our science predictive, to fulfill the promises of “post-genomic” biology for biotechnology and molecular medicine. Bioinformatics builds the toolbox of this science with methods that make biological information computable. Computational biology is bioinformatics’ goal: we hope to advance our understanding of life through computational analysis, modeling, and prediction.

The Bioinformatics and Computational Biology specialist program - provides a balance between its foundational subjects and covers advanced topics in both the theoretical and the life-sciences. It aims to train future leaders in the field who will develop original, creative problem-solving strategies at the intersection of theory and experiment. The program draws on the University’s state-of-the-art facilities across several departments, as well as being firmly embedded in a comprehensive landscape of graduate and postgraduate research in one of the University’s priority areas. Graduates of the program would typically pursue graduate studies in any of the participating departments: Computer Science (from the biocomputing stream, see below), Biochemistry, or the biological disciplines (from the bioanalyst stream). Their professional careers may span a wide range of opportunities in academic research, but also entering into medical school, and biotechnology careers in drug-development, agrotechnology or even patent law.

The Bioinformatics and Computational Biology Program is jointly sponsored by the Departments of Biochemistry, Cell & Systems Biology, Computer Science and Ecology & Evolutionary Biology. Enrollment is limited and selection is based on performance in the required first year courses.

Specialist program:

(16.5 full courses or their equivalent)

First Year: MAT135Y1/MAT137Y1/MAT157Y1; (CSC107H1/CSC108H1, CSC148H1)/CSC150H1; CSC165H1; CHM151Y1/(CHM138H1, CHM139H1); BIO150Y1/(BIO120H1, BIO130H1); writing requirement (0.5 credit, see Note 2 to Comprehensive Program in Computer Science)

Second Year: MAT223H1/MAT240H1; STA247H1; STA248H1; CSC207H1; CSC236H1/CSC240H1; BCH242Y1; BIO250Y1; BIO240H1; BIO241H1

Third Year: CSC263H1/CSC265H1; CSC321H1/CSC343H1; CSC373H1/CSC375H1; BCH441H1/BIO472H1; MGY311Y1/(BIO260H1, BIO349H1)

Fourth Year:

Bio Analyst Stream (preparation for life-science graduate programs) BCB410H1; BCB420H1; CSC411H1; five half credits from (BCB430Y1, BCH335H1, BCH340H1, MGY420H1, MGY425H1, MBY428H1, BCH422H1, BCH426H1, BCH440H1, MGY460H1, BIO460H1, BIO473H1, BOT421H1, BOT450H1, BOT458H1)

Bio Computing Stream (preparation for computer-science graduate programs) BCB410H1; BCB420H1; CSC411H1; CSC336H1/CSC350H1; one half credit from (MGY420H1, MGY425H1, MBY428H1, BCH422H1, BCH426H1, BCH440H1, MGY460H1, BIO460H1, BIO473H1, BOT421H1, BOT450H1, BOT458H1); three half credits from (BCB430Y1, CSC324H1, CSC363H1, MAT244H1, CSC310H1 CSC321H1,CSC343H1, CSC412H1 CSC456H1)

Molecular Biophysics (Science Program): See Physics

Biochemistry Courses

For details on BCB courses, see www.biochemistry.utoronto.ca/bcb

For more information please contact the BCB Program Coordinator: Boris Steipe (boris.steipe@utoronto.ca).

Practical introduction to concepts, standards and tools for the implementation of strategies in bioinformatics and computational biology.

Current approaches to using the computer for analyzing and modeling biology as integrated molecular systems. The course complements an introductory Bioinformatics course such as BCH441H1. (Enrolment limited).

An opportunity for specialized individual research in bioinformatics and computational biology by arrangement with the course coordinator and a supervisor.

NOTE***Students that do not meet the Subject Post requirements for PE/AE courses must email Dr. Roy Baker for permission to take the course.

Proteins, enzymes, membranes and the metabolism of carbohydrates and lipids. This course is intended for students who are NOT taking BCH242Y1 as part of their program.

An introductory course that will serve as the foundation for BCH courses taken in Third and Fourth years by students specializing in biochemistry and related specialist programs. The major topics include protein structure, enzyme mechanisms, carbohydrates, metabolism and bioenenergetics, lipids, membranes, cellular and molecular biology. Please note that there are four laboratories in this course. 

Credit course for supervised participation in faculty research project. Details here.

Nucleic acids and flow of information in biological systems. Information storage and transmission by nucleic acids, as well as new molecular technologies will be discussed. Registration in one of the tutorial sessions is mandatory. Note: Students that have a SDF in BCH210H1 are not permitted to take BCH311H1 until a final passing mark appears on the transcript. BCH2** WITH COURSE EXCLUSION TO BCH210H1 meets the prerequisite requirement for BCH311H1.

Proteins are the main functional units of the cell. In this course, a detailed overview of protein structure, stability, folding, and protein-ligand interactions will be given with strong emphasis on discussing the basic principles in the field. Biophysical methods as well as theoretical approaches to studying protein stability and folding will be presented. Finally, proteomics approaches to map protein-protein interactions will be discussed.

This course reinforces theoretical principles through experiments that encompass pH and buffers, spectrophotometry, chromatography, electrophoresis and enzyme kinetics. Intended for students who are not proceeding further in biochemistry. It is highly recommended that students take this course in their third year as space is limited and priority will go to third-year students. cGPA of 2.5 is required for non-Biochemistry Majors and Specialists. This course will be offered in the FALL & WINTER terms. No enrolment will be permitted five days after the start of class. (Enrolment limited)

An introduction to laboratory techniques of modern biochemistry. Experiments illustrate and develop the concepts described in lecture courses, and prepare the student for advanced training in biochemical laboratory techniques. (Enrolment limited)

This course provides increased real-world research opportunities to undergraduates who have completed second year. Students can take advantage of the resources and expertise of the over 50 faculty researchers within the department. It will give students an appreciation of the scientific method that comes from intensive experimentation and it will enhance students understanding of theoretical concepts learned in other courses through a better understanding of the experimental approaches upon which those theories are based. It also will provide an environment that involves one on one contact with faculty members. The experience gained in this introductory research project will enhance the student experience in intermediate and advanced level research project courses that our department offers. Students must have a minimum cGPA of 3.0.

This course is held in the fall term and will provide increased real-world research opportunities to our undergraduates. This course, which will take advantage of the resources and expertise of the over 50 faculty researchers within the department, will enhance our program in several ways. It will give students an appreciation of the scientific method that comes from intensive experimentation. It will also enhance students understanding of theoretical concepts learned in other courses through a better understanding of the experimental approaches upon which those theories are based. It will provide an environment that involves one on one contact with faculty members. In addition, the experience gained in this intermediate research project will enhance the student experience in the advanced level research project course BCH473, that our department offers. BCH373H1 can be combined with BCH375H1. Students must have a minimum cGPA of 3.0.

This course provides an opportunity to perform specialized research in biochemistry under the direct supervision of Biochemistry Department faculty. (See BCH373H1).

An introduction to fundamental laboratory techniques in modern biochemistry. Experiments illustrate and develop the concepts described in lecture courses and serve as a foundation for more advanced training in biochemistry laboratory courses.

This course builds upon the fundamental laboratory techniques acquired in BCH377H1.  Students gain hands-on experience in experimental design and data analysis, exploring numerous modern experimental techniques used in biochemistry research laboratories.

Note
Students who have completed University of Toronto at Mississauga’s CHM361H5 AND362H5 may enroll in 400-series lecture courses if they obtain permission of the Department

Structural features of membrane proteins and methods of analysis. Function of membrane proteins as transporters, channels, pumps and receptors. Molecular aspects of disease processes linked to membrane proteins.

Theory and practice of modern biophysical techniques as applied in the study of structure and function of macromolecules; emphasis on protein X-ray crystallography, NMR, electron microscopy and other spectroscopic methods; discussion of selected examples.

A variety of questions relating to signal transduction are investigated. How is calcium regulated in the cell and how does calcium regulate cell function? How are extracellular signals received and transmitted by intracellular proteins to control cellular proliferation and differentiation? What signaling pathways are triggered by insulin?

This course provides a focused study of concepts in thermodynamics, statistical mechanics and quantum mechanics through examples dealing with important current problems in molecular biophysics. Concepts in thermodynamics and statistical mechanics will be surveyed through applications to protein folding, while principles of quantum mechanics will be emphasized through a study of nuclear magnetic resonance spectroscopy.

Mechanisms of translation initiation and translational control, ribosome assembly and structure. Protein folding and molecular chaperones. Protein targeting and transport. Regulation of protein degradation.

This course covers computational methods and internet resources in modern biochemistry and molecular biology. The main topics include: sequence and genome databases, sequence alignment and homology search, use and interpretation of molecular structure, and phylogenetic analysis. Assignments focus on competence building with essential, web-based bioinformatics tools. Tutorials are optional and will be offered based on needs. For curriculum details see: www.biochemistry.utoronto.ca/undergraduates/courses/BCH441H/wiki/

This course examines the molecular details of the secretory and endocytic pathways in the cell. Some of the specific topics covered will include protein translocation into the ER, chaperones and protein folding in the ER, retrotranslocation and protein degradation, the Unfolded Protein Response (UPR), vesicle biogenesis and ER-Golgi transport, regulated secretion, basic concepts in endocytosis and protein sorting in polarized cells.

Advanced principles and concepts of cell biology are covered including the structure, biogenesis, and dynamic behavior of cell organelles. The specific contributions to the life and death of the cell are highlighted. Signaling events that integrate cellular communication are discussed. Specifically, the interplay between the Endoplasmic Reticulum, Peroxisomes and Mitochondria is highlighted. Mitochondrial biogenesis and membrane dynamics as they relate to apoptosis and cellular signaling/integration are presented as they relate to human disease. State-of-the-art imaging techniques and the contributions of cell biology to modern day advances in medicine are also presented.

Principles and concepts of cell biology are covered including the structure, molecular organization and dynamic interactions of cells with each other and the extra cellular matrix during cell migration and cell adhesion. The role of cytoskeletal components and cell surface receptors in these processes and in membrane traffic will be addressed. Signaling pathways initiated by cell-cell interactions during normal and pathological development will be discussed.

This course will examine the fundamental concepts of evolution with an emphasis on molecular evolution. We will discuss selected controversial topics such as molecular clocks, alternative splicing, junk DNA, random genetic drift vs. natural selection, the Three Domain Hypothesis and whether humans are evolving. We will examine various evolutionary hypotheses that scientists are proposing as alternatives to the Modern Synthesis.

This course examines the structure and function of the cell nucleus. Topics that will be covered are the organization of the genome and nucleus, junk DNA, the filtering of information found in the genome into biologically relevant molecules such as mRNA and the export of these products from the nucleus into the cytoplasm. We will also investigate the role of the nucleus in a diverse number of biological processes such as cell polarity, muscle and neuronal development, and aging.

Experiments demonstrating modern concepts of biochemistry and molecular biology. (Enrolment limited)

This course provides an opportunity for students who have completed third year to perform specialized research in biochemistry under the direct supervision of Biochemistry Department faculty. (See BCH373H1).

Research in a particular area of biochemistry, by arrangement with the Department and the instructor concerned. Students must have a minimum GPA of 3.0.

This seminar course will foster close interactions between students and Faculty and encourage in depth discussion not only of results but the ways the results were presented and the rationales for experimental design. Critical thinking skills will be developed, as will presentation skills, as students become presenters of results and take on the role of scientist presenting and analyzing new findings. Writing skills will be developed through an essay assignment. Students within the audience will also have access to the experimental papers and be encouraged to pose thoughtful questions about research and the ways that research can be communicated within the scientific community. Thus the new seminar course will foster an appreciation of scientific writing and give students a venue to develop their communication skills. The goal of the seminar course is to improve both the written and oral scientific communication skills of our Specialist students, as well as to increase their knowledge of key papers in Biochemistry.