4th Year Biochemistry Courses

Biochemistry Undergraduate Student Society

BCH422: Membrane Proteins: Structure and Function

Speaker: Dr. Roy Baker

Pre-requisites: BCH210H/242Y, BCH311H/MGY311Y/CSB349H/PSL350H

Timetable: Fall term, TR11

Course breakdown: Two assignments worth 25% each, a mid-term worth 25%
and a final exam worth 50% of the final mark.

Course marks: Last year, 36% of the class had A’s and 35% B’s.

Course size: Around 70 each year

Other notes:

- Course textbook: Membrane Structural Biology by Mary Luckey, Cambridge

University Press (2008).

- This course covers the structure and functions of membrane proteins –

including transporters, pumps etc.

- Membrane protein diseases and experimental methodologies will be

discussed

- Assignments are problem solving problems, and past assignments are

available online

BCH425: Structural Biology: Principles and Practices

Speaker: Dr. John Rubinstein (course instructor)

Pre-requisites: BCH210H/242Y, CHM220H

Timetable: Fall term, TR10

Course breakdown: 25% problem sets, 25% midterm, 50% final

Course marks: Last year, 43% of the class had A’s and 41% B’s.

Course size: Not mentioned

Other notes:

- No textbook required

- The course is aimed at helping students understand structural biology and its
challenges

- The three main focuses are: X-ray crystallography, NMR, and Electron
cryomicroscopy, with some lectures touching upon atomic force microscopy
and solid-state NMR.

- Dr. Rubinstein placed a large emphasis on the fact that the course requires
no memorization of pathways or equations at all, but the focus is on problem-
solving instead

- Assignments and exams weights are proportional to number of lectures spent

on each topic.

- Dr. Rubinstein mentioned that pre-requisites were intentionally set lower to

allow students from the chemistry, physics and engineering departments to
enrol.

BCH426: Regulation of Signalling Pathways

Speaker: Dr. Roy Baker

Pre-requisites: BCH210H/242Y, BCH311H/MGY311Y/CSB349H/PSL350H

Timetable: Fall term, TR11

Course breakdown: 35% midterm, 65% final exam last year, however Dr. Attisano
will be reducing the weight of the final exam and adding in a second evening
midterm for 2009 – 2010.

Course marks: Last year, 43% of the class had A’s and 41% B’s.

Course size: Between 60 – 70 students

Other notes:

- A popular course due to its broad application

- This course can be considered a sequel to metabolism

- The following pathways/topics will be covered:

o TGF-β , carbohydrate, and calcium pathways

 o Protien-coupled receptors

o Signalling mechanisms of lipids [using a disease-oriented approach]

- Dr. Baker placed an emphasis on having Dr. David MacLennan teaching part
of this course.

- This course does not use a textbook, but rather handouts and suggested
reading materials from literature reviews & primary papers.

BCH427: Advanced Molecular Biophysics

Speaker: Dr. Roy Baker

Pre-requisites: CHM326H/PHY355H, CHM328H

Timetable: Fall term, R11-1

Course breakdown: New course

Course marks: New course

Course size: New course

Other notes:

- New course aimed at merging biochemistry and physics.

- Dr. Baker recommends contacting the course co-ordinator (Dr. Lewis Kay) if
interested.

JBI428: Molecular Immunology

Speaker: Dr. David Isenman (course co-ordinator)

Pre-requisites: BCH210H/242Y, IMM344Y/335Y

Timetable: Fall term, TR9

Course breakdown: 33% midterm, 67% final exam.

Course marks: Last year, mean was 72%, median 75% (1/3rd A’s, 2/3rd B’s)

Course size: 21 students last year

Other notes:
 - The course focus is on experimental approaches that led to the discoveries in
IMM334/335, especially on relevant techniques still used today.

- Exams are problem-based and ask you to interpret data and design
experiments.

- Much less memorization as compared to IMM334/335

- The course is composed of four blocks:

o Antibody structure, function & biotechnologies

 Ab structures, Ab affinity measurements, avidity, monoclonals,

phage-display, Ab effector functions [stories of how Fc, C1q
interactions were found, including crystal structures]

o Complement biochemistry & immunobiology

 C1 & MBL/MASP activation mechanisms, covalent binding of C3

& C4, regulatory molecules of complement, complement
receptors, molecular adjuvant role of complement in B cell
response

o MBC & T-cell receptors

 T cell receptor & MHC I/II structures, antigen processing &

presentation by MHC I & II. Antigen processing in dendritic cells,
T cell receptor signalling, co-stimulation mechanism

o NK cells

 NK receptor families of molecules & mechanisms of self/non-self

recognition, cytolytic killing mechanisms

- There is no required textbook for this course, but the IMM334/335 text may
be useful

- Final exam is not cumulative.

- 3 years of previous exams & review sessions prior to both exams are
available.

BCH440: Protein Biosynthesis

Speaker: Dr. John Glover (course co-ordinator)

Pre-requisites: BCH210H/242Y, BCH311H/MGY311Y/CSB349H/PSL350H

Timetable: Spring term, TR9

Course breakdown: 33% midterm (x2), 33% final exam.

Course marks: Last year course average: 78%, previous years: 72%.

Course size: 40 – 45 students

Other notes:

- Learning Material(s): Handouts of slides, posted supplementary notes &

slides; suggested readings from primary literature

- Course content: Nuclear trafficking  nucleus (tRNA, ribosomes)  cytosol &

proteins in cytosol  nucleus; translation initiation & elongation; organelle
import (mt, peroxisomes, ER, etc); molecular chaperones; misfolding
diseases; protein damage/aging  alzheimers, diabetes, etc; Protein turnover

- May do non-compulsory quizzes on blackboard to help with understanding

- Final exam is NOT cumulative.

BCH441: Bioinformatics
Speaker: Dr. Boris Steipe (course co-ordinator)

Pre-requisites: BCH210H/242Y, BCH311H/MGY311Y/CSB349H/PSL350H

Timetable: Fall term, MR12, with M1 tutorial

Course breakdown: 16% assignments, 32% quizzes, 10% group project, 2%

participation, 40% final exam.
5 assignments & 5 quizzes, lowest mark from each is dropped in the calculations.

Course marks: Last year, median was just above 78%

Course size: 58 students last year

Other notes:

- “[There is] no modern biochemistry w/o bioinformatics” – Dr. Steipe

- Learning Material(s): Recommended textbook; Internet access is required;

Google groups (mailing list), course wiki  faster feedback from assignments;
3-D structures with stereo-vision

- Course Content:
 o Sequences: Abstraction, databases & analysis

o Homology: Alignments & searches

o Structures: Databases & interpretation

o Genomics: Genes, genomes, comparisons

o Function: Description, regulation & annotation

o Phylogeny: Trees & inference

o De-emphasizing computational systems biology is moved to BCB420

(spring w/ BCH441 pre-req)

- More on evaluation:

o 5 hands-on assignments (bi-weekly)  point submissions format, not

essays. Do-able in a day. See wiki for assignments

o Group project (was sequence analysis last year)  combine results

from different resources & interpretation

o Monday’s scheduled tutorial time used as quiz writing, take up, &
discussion time. Tests/quizzes are closely aligned with assignments.

- Some student feedback is posted on the course wiki page for those interested

BCH444: Protein Trafficking in the Secretory & Endocytic

Pathways
Speaker: Dr. Allen Volchuk (course co-ordinator)

Pre-requisites: BCH210H/242Y, BCH311H/MGY311Y/CSB349H/PSL350H

Timetable: Spring term, TR10

Course breakdown: 25% midterm, 50% final, 25% written assignment (see notes).

Course marks: Last year, average was in mid-70’s

Course size: 31 students last year

Other notes:

- No textbook, most material is based on lecture notes/slides and primary

articles.
 - The course focus on the mechanisms of how secretory protein synthesis,
targeting to ER and transportation out through the Golgi bodies as well as
experimental systems used to study these processes.

- The written assignment is a critique of an assigned scientific paper – Dr.

Volchuk expects a 2 page report on the paper, the techniques used and
pros/cons of the study.

- Final exam is NOT cumulative.

BCH445: Organelles and Cell Function

Speaker: Dr. Angus McQuibban (course co-ordinator)

Pre-requisites: BIO250Y, BCH210H/242Y, BCH311H/MGY311Y/CSB349H/PSL350H

Timetable: Spring term, W2-4

Course breakdown: 30% midterm, 20% quiz on academic paper, 50% final exam.
(Dr. McQuibban is considering adding student presentations for 2009-2010, so the
breakdown may change.)

Course marks: Not mentioned. We hear it’s similar to other 4th year BCH courses.

Course size: 24 students last year

Other notes:

- Learning Materials: No textbook – most material is from primary literature

within the past 3-4 years

- Course content: Covers all of cell biology; Dr. McQuibban is particularly

interested in and will focus on the cross-talk among mitochondria, ER and
peroxisomes. The major focus is on apoptosis.

- This year, he will try to include a presentations component based on current

published literature

BCH446: Membrane Dynamics of the Cell Surface

Speaker: Dr. Roy Baker

Pre-requisites: BIO240H/250Y,
BCH210H/BCH242Y/BCH311H/MGY311Y/CSB349H/PSL350H and cGPA > 2.5 for non-
Biochemistry Major/Specialist students.
Timetable: Fall term, W2-4

Course breakdown: New course

Course marks: New course

Course size: New course

Other notes:

- This used to be offered as a 3rd year course

- The focus is on cell surfaces – events at the cellular membrane and

interactions of cells with each other and the external environment.

- Dr. Baker expects the course to have 1-2 midterms and a final exam

BCH479: Advanced Seminar in Biochemistry

Speaker: Dr. Roy Baker

Pre-requisites: BCH335H, BCH340H, BCH371H and permission of Department (see

notes)

Timetable: Fall term, T1-3. Note: Timetable incorrectly lists this as being offered
in the spring term with time TBA.

Course breakdown: 20% presentations (x2), 10% participation, 50% essay.

Course marks: New course

Course size: 6-8 students.

Other notes:

- Course will be led by four professors: Dr. Reithmeier, Dr. Williams, Dr. Wilde
and Dr. Pulleyblank. Each will cover three weeks of the term.

- Students will present two critiques of modern papers over the course of the
term.

- Students will consult with one of the four professors before the course starts
to get a direction and discuss presentation topics, and these one-to-one
meetings are expected to continue on a semi-regular basis throughout the
term.
- There will be a final essay worth 50% due at the end of the course, but Dr.
Baker expects that students should be able to write it halfway through the
term based on meetings with professors.

- The course is designed to improve students’ communication and writing

skills, and offers very close interactions with mentors.

- Priority is given to BCH specialists first.

- Depending on enrolment, the department may hold interviews before the

school year starts to pare the course down to 8 students.