COURSES

Choose from a diverse set of courses to support all biochemistry specializations.

courses

Please see the Biochemistry Graduate Program Handbook for more information.

The graduate courses offered by the Department cover a broad range of biochemistry. In addition, courses in other departments/programs, notably Biology, Chemistry, Medical Sciences, Physics and Astronomy, and Chemical Biology may be allowed for graduate credit. Students must consult with their supervisor when selecting courses. The courses are subsequently approved by our Graduate Admissions Committee.

Permission to Register in a Course

Enrolment in all courses is subject to permission from the respective departments. Lisa Kush (kushL@mcmaster.ca) is the Biochemistry & Biomedical Sciences Department contact. Students are to contact outside departments directly to obtain permission to enrol in non-Biochemistry courses. Class sizes are usually small for graduate courses (some programs allow no more than 10 students to enrol) so it is important that students indicate their interests early.

*Note: 700 Level chemistry courses equal one-quarter credit.

The following 700-level courses (half course credit) are available to graduate students only:

BIOCHEM 720 - Biochemistry Colloquium

Instructor:   Brian Coombes
Term 1 & 2:   Sept 2017 – April 2018
Limited to students enrolled in their 2nd year of our Master’s program.

(Email: kushl@mcmaster.ca for permission)

The aim of this course is a detailed examination of the student’s own area of research. Students will prepare a review article describing the current state of their field in the format employed by the journal “Trends in Biochemical Sciences”. In addition to this, students will give a seminar on their research, including necessary background information in the course of the Departmental Seminar Series. Following that, the student will answer questions from selected faculty members.

BIOCHEM 711 - Special Topics in Biomolecular Sciences: Immunometabolism

Instructor:  Jon Schertzer
Term 1:   Sept – Dec 2017
Limited enrollment: 10 students

(Email: kushl@mcmaster.ca for permission)

This course will review contemporary concepts in immunometabolism. The main goal of this course is to examine the links between metabolic and immune systems in the progression and consequences of chronic diseases. These topics may include: immune-mediated changes in endocrine control of metabolism and how metabolic flux contributes to immune regulation. Students will participate in the presentation of the course material and be evaluated on class presentations, succinct literature review and research proposals.

BIOCHEM 711 - Special Topics in Biomolecular Sciences: Pharmacology & Cell Biology

Instructor:  Nathan Magarvey
Term 2:   January – April 2018
Limited enrollment: 10 students

(Email: kushl@mcmaster.ca for permission)

This course will cover topics of current interest in the areas of Systems Pharmacology and Chemical Biology. A particular focus will be placed on the properties of drugs and natural chemicals and their interaction with living systems. Select examples will be discussed on how to probe the mechanism of action and global pharmacological properties. Natural products small chemicals will remain a start point for discussions and learning how best to generate new targeted chemotherapies based on systems pharmacologic principles.


BIOCHEM 732 - WRITING FOR SCIENCE

Instructors:  Lesley MacNeil
Term 2:    January – April 2018
Limited enrollment: 12 students – COURSE IS FULL

This course will provide students with the tools needed to become better, more effective science writers.  Issues of style, content and organization will be addressed. Topics covered include: crafting better sentences and paragraphs, effectively communicating your message, creating effective figures and diagrams, and writing for a number of different audiences. Students will learn to write a lay summary, a research article and a funding application.

The following 600-level courses (half course credit) offered for graduate credit consists of the corresponding 400-level undergraduate course plus additional work, usually in the form of a written assignment.

Gene Regulation and Stem Cells and Development 6E03

Instructors: M. Bhatia, B. Doble, S. Singh, K. Hope (Term 1)

Recombinant DNA techniques: theory and application to the study of gene function and evolution and to disease diagnostics and gene therapy. Current concepts of gene regulation at different levels.

Molecular Membrane Biology 6N03

Instructors: R. Epand and R. Bishop (Term 2)

Properties and structures of membranes, molecular components of biological membranes and their interactions, strategies for signal transduction cascades, hormones, receptors.

Biochemical Pharmacology 6Q03

Instructor: R. Gupta (Term 1)

Introduction to the basic concepts of pharmacology.  Mechanisms of action of antibacterial, antiviral, antifungal and anticancer drugs, toxins and how cellular resistance to such agents develop.  Applications of drug-resistant mutants for genetic, biochemical, pharmacological and cell biological studies.

Introduction to Molecular Biophysics 6S03

Instructor: P. Higgs (Term 1)

This course is administered by the Department of Physics and Astronomy. A presentation of recent contributions made to the fields of molecular and cell biology by the use of physical approaches. Topics include physical properties of biomolecules, protein folding, molecular motors, cell motion and cell adhesion. Emphasis on the critical evaluation of current research literature.

Genomes and Evolution 6Y03

Instructor: P. Higgs (Offered Term 2, every other year)

Molecular evolution and comparative analysis of genomes. Bacterial evolution, phylogenetics, origins of eukaryotes. Organelles and their genomes. Comparison of the human genome with other species. Use of microarrays and proteomics.

(NOT OFFERED IN 2016-2017 BUT POSSIBLY IN 2017-2018)

Mechanism of Enzyme Action *707

Sequence of molecular events occurring during catalysis by enzymes. Nature of intermediates and active site residues. Possible factors involved in rate-acceleration. Enzyme kinetics.

Signal Transduction: Receptors, G-proteins, Target Enzymes ... *708

Signal Transduction: Receptors, G-proteins, Target Enzymes and Second Messengers

(same as Medical Sciences *708)

The topics covered will include the mechanisms of activation of the nicotinic

cholinergic receptor, G-protein-coupled receptors, G-proteins, adenylyl and guanylyl cyclases, phospholipase C and phosphoinositide 3-kinases and the roles of cAMP, cGMP, inositol phosphates, Ca2+, diacylglycerol and 3-phosphoinositides as second messengers. The targets of these second messengers will also be discussed. The course will be based on recent review articles and important current papers. After six sessions, with faculty lectures and student presentations, the students will spend 5 weeks of inquiry on a related topic and each write a paper for evaluation by faculty and for presentation in summary in a symposium.

Signal Transduction: Dynamic Mechanism of Action of Growth Factors ... *709

Signal Transduction: Dynamic Mechanism of Action of Growth Factors and Nuclear Receptors

The topics covered will include: Ras and GTP binding protein families, MAP kinase cascades; T-cell and B-cell activation; nuclear receptors for steroid and thyroid hormones. The course will be based on recent review articles and important current papers.

Special Topics in Proteins *710

In this course, we will discuss the potential and applicability of cryo-electron microscopy (cryo-EM) as a structural biology technique. From the structure of ribosome intermediates in the process of translation to the structure of viruses, cryo-EM has played an instrumental role in our current understanding of protein function. In addition, cryo-EM is an ideal tool to study the structure and function of proteins in the context of physiologically relevant macromolecular assemblies or even the entire cell. The course will provide several lectures on the principals of cryo-electron microscopy and image processing and the students will be also expected to present a major research paper in this field.

Special Topics in Biomolecular Science: Microbial Pathogenesis *711

Instructor:  Tim Gilberger (Jan – April 2012)

The main goal of this course is to provide an introduction into diseases caused by parasites with strong emphasis on cell biology. It will elucidate fundamental concepts in parasitism, cell-cell interaction, host cell transformation, immune evasion and host susceptibility & resistance. The focus will be the malaria parasite, its complex biology and its subversion of the human defense mechanism.

Special Topics in Bacterial Cell Surfaces *711

A combination of lectures, inquiry and journal club formats will be used to examine current research in the area of bacterial cell surfaces. Topics that will be covered include surface macromolecules (lipopolysaccharide, capsules, peptidoglycan, teichoic acids); secretion and motility systems; trafficking of proteins to specific compartments (the Sec, Tat, Lol systems, Omp85, sortases); and signal transduction (chemotaxis, two-component regulators). Students will be evaluated through assessment of written and oral presentations.

Special Topics in Microscopy and Photonics *711

A wide variety of topics in biophotonics will be introduced in this one-term course.  Each student will explore an assigned topic in biophotonics, with a view to providing a broader understanding of the use of biophotonics in a range of research questions.

The Molecular Biology of Glucose Metabolism *711

This course will focus on recent developments in the molecular biology of glucose transport and metabolism with special focus on disorders associated with diabetes mellitus and insulin resistance.

Enzyme Catalytic Mechanisms *713

An examination of enzymes’ catalytic strategies, including strategies for promoting catalysis, enzymatic intermediates, co-factors as well as the methods used to probe mechanism. Examples from the current literature will be used to demonstrate each concept.

Special Topics: Pathogenesis in Tropical Diseases *723

Instructors: Tim Gilberger/Nathan Magarvey (Term 2)

Objectives:  The main goal of this course is to provide an introduction into tropical diseases caused by parasites. It will elucidate fundamental concepts in parasitism, host cell transformation, immune evasion and host susceptibility & resistance. The focus will be the malaria parasite, its complex biology and its subversion of the human defense mechanism.   Classes will consist of a 30 min lecture, general discussions and journal-club style presentations by class members (2 presentations per class). Papers for presentations will be selected from a provided reading list. The expectation is that students will “select and adopt” one tropical disease and prepare to chair and discuss aspects of it during the journal club. All papers in the reading list are mandatory reading. Each student will give onepresentation during the course, which will be based on an article from primary literature. The presentation will focus on recent highlights and technological advance in the area of molecular parasitology preferentially malaria, sleeping sickness and leishmaniasis. The student will select the paper for presentation.  The students will embark on a gene-to-function journey: Each student will select one gene from a list of 15 encoded in the genome of the parasite. This gene and its product will be analyzed in silico in detail using all information imbedded in the PlasmoDB database (www.plasmodb.org). An introduction in the use of this database will be provided.  Each individual student will summarize its findings and use the information to write a short project proposal not longer than 10 pages (double spaced; not including references). The analysis of the gene and the framework of the proposal should be discussed with Tim prior commencing writing.

Molecular Mechanisms of Membrane Functions *725

The molecular basis of the biological activity of membranes at an advanced level.  Topics include: bioenergetics, transport, membrane biogenesis and turnover, signal transduction, cell surface interactions and membrane disorders.

Protein Structure Determination using NMR & X-ray Crystallographic ... *727

Protein Structure Determination using NMR & X-ray Crystallographic Techniques

Critical examination of classic and current papers in structural biology. The course will cover methods and challenging techniques often used to investigate the structure, dynamics and interactions of proteins and protein complexes, as well as, providing students the opportunity to practice their presentation and discussion skills.

Computational Biochemistry *730

This course will provide a brief introduction to biochemical databases, biological data mining and tools for sequence analysis. This will be followed by more detailed description of computational methods of molecular modeling, ligand docking, and analysis of ligand-receptor interactions. Facilities of the Educational Computing Lab will be used to train students on applying WWW resources of biological information and molecular modeling software in a biomedical lab.

Stem Cells and Regenerative Medicine *731

Stem cells hold immense experimental potential as model systems for human disease and development that are difficult to ascertain in cell lines or in the mouse. Arguable, the most impactful role of human stem cells is for tissue repair that becomes damaged from disease or injury, examples included diabetes and spinal cord injury. This utility of stem cells is heavily seeded in new approaches to the clinical called “regenerative medicine”. However, there are many stem cell types that may be specific to certain applications, new technologies involved with stem cell delivery and differentiation that require elucidation before these stem cell based replacement therapies can be robustly brought to the bedside. The underlying biology that defines stem cells, and their potential applications to human health will be discussed broadly to better define the current successes and future limitations of regenerative medicine using human stem cells.

Course Requirements

  • M.Sc. Two one-semester 700-level graduate courses.
  • Ph.D. There is no formal course requirement for doctoral students. Those students who wish to do so may participate in any relevant course offerings in BBS or other departments.

Students must complete courses with at least B- standing. At least one full, 700-level graduate course (or two half courses) must be completed, which must include at least one half, 700-level graduate course in Biochemistry. Supervisory committees may require a student to take courses in addition to those prescribed by departmental regulations. Students may take 600-level courses however these do not count towards degree requirements. Under normal circumstances a student who fails to obtain B- in a prescribed course is asked to withdraw from the program. Those allowed to remain in the program must either repeat or replace the failed course. A failing grade in a prescribed course remains on the transcript.


All graduate students are required to pass the following courses to be “clear to graduate” or to continue into subsequent academic session and we urge all students to register for and take this course at their earliest opportunity.

SGS 101# - Academic Integrity/Research Ethics

ALL new students must complete the “Academic Integrity and Research Ethics Course” administered by the School of Graduate Studies within the first MONTH after their admission into graduate studies at McMaster University. The purpose of this course is to ensure that the standards and expectations of academic integrity and research ethics are communicated early and are understood by incoming students. A graduate student may not obtain a graduate degree at McMaster without having passed this course. In the event that a student fails this course, they must retake it at the earliest opportunity.

To access the course material after you enroll, please complete the following steps:

  • Log in to “Avenue to Learn” at: http://avenue.mcmaster.ca/. Your student MacID and password are required.
  • Under “My Courses”, you will have an entry for “SGS 101”. Click on the link.
  • Click the “Content icon” at the top of the page.
  • Content must be viewed before the final quiz is released.
  • To access the quiz, click on the “Assessments icon” at the top of the page. The drop down box will then show quizzes; click on the link.
  • Students must successfully pass the quiz with a mark of 7 out of 10 or greater.
  • The student is informed of their mark on the quiz immediately after submitted electronically.

SGS 201# - Accessibility for Ontarians with Disabilities Act

SGS 201 – Accessibility for Ontarians with Disabilities
The Ontario government has enacted a Customer Service regulation of the Accessibility for Ontarians with Disabilities Act, 2005, which came into effect with the start of 2010. Senate passed the requirement for all graduate students to complete this training.   The AODA Office maintains the course content and a record of all McMaster students who have taken the course. Completed results will appear on student records.   The course content is offered through: http://www.mcmaster.ca/accessibility/ (click AODA CUSTOMER SERVICE TRAINING). Once you have completed SGS201, AODA will send you a confirmation email.   Please forward your email to kushL@mcmaster.ca and keep a copy for your record.

Log in to: https://mosaic.mcmaster.ca

 

  • Click on: Student Center tab (at the top)
  • Search tab
  • Course career: select “Graduate” from the drop down menu
  • Term: select appropriate term “2016 Fall”
  • Course Subject: enter “SGS”
  • Course number: 201
  • Click: SEARCH
  • Take note of the course number (ie 15828)
  • Click on: Enroll tab (at the top)
  • Enter course Section “2016 Fall”
  • Continue
  • Save
  • LOG IN TO AVENUE TO LEARN:   http://avenue.mcmaster.ca/
  • Select a course (drop down menu at the top) – AODA online training
  • Students must answer all 6 questions correctly.
BIOCHEMISTRY GRADUATE PROGRAM RESEARCH ETHICS COURSE

The department holds a one-day departmental workshop on research ethics, data presentation and scientific integrity. This is held in December and is mandatory for all first year graduate students.