MGY 311Y: Molecular Biology
Monday, Wednesday, Friday at 9-10 am, Rm 2172 MSB
(except test dates which start at 8:30 am)


Course Coordinator
Professor Rick Collins
Department of Molecular Genetics

Course content
The purpose of this course is to show you how science is done in the field of molecular biology. The emphasis will be on how we come to know something, rather than just what we know. Subject material includes: DNA replication, DNA repair and mutation, recombination, transcription, RNA processing, the genetic code and tRNA, translation, regulation of gene expression, functional genomics (see Learning Outcomes).


The course prerequisites are BIO230H and BCH242Y, however genetics (BIO260H or HMB265H) will help. We suggest that students without genetics may want to invest in a genetics textbook if they have problems with some of the genetic terminology.

See Learning Outcomes for MGY311Y

There are two term tests, an essay, and a final exam in this course: In 2012-2013 the distribution is 25% Nov term test, 20% Jan term test, 25% essay, and 30% final exam.

The term tests, given in class (except with 8:30 am start), will be held Nov. 14, 2012 and Jan. 25, 2013.


Term test #1 is worth 25% of your final grade, and will cover sections I through III (nucleic acids, DNA replication, DNA repair)


Term test #2 is worth 20% of your final grade and will cover sections IV and V (recombination, transcription) (see schedule).

The essay mark contributes 25% of your grade. See essays for more information on their preparation and submission.

The final exam, worth 30% of the final course mark, will be based primarily on material covered in sections VI through VIII (RNA processing to Genomics, inclusive), but concepts and general principles from the entire course may be examined. Copies of old final exams from MGY311Y are available on the Faculty of Arts & Science exam website (A&S final exams -search for MGY311Y). Exams and tests will consist of multiple choice questions and short answer essay questions depending on the instructor.

Course tools and class attendance
MGY311Y uses the Blackboard website, accessed through the U of T Portal, to post information and grades, and to contact students (by email) during the course. Lecture handouts, notes, and additional readings may be included; this will depend on each individual instructor. You should check your utoronto email account regularly for announcements related to MGY311Y.

As mentioned in the "Learning Outcomes" section, many of the lectures are designed to show you how to think about molecular biology, not just to memorize things. We hope that you will find this a refreshing, albeit challenging, experience. We strongly encourage you to bring your active and interactive mind to each lecture, rather than depending on audio recordings or borrowing notes from classmates. Learning how to think in real time will improve your understanding of the material and your performance in the course. Recording of lectures is permitted for personal use (e.g. reviewing for exams) or for sharing with classmates. You must obtain written permission from each instructor to post lectures on Biome or any other website.

If you encounter difficulties with the material in any part of the course please consult the lecturer. All of us are happy to meet with you to go over our lectures. You can set up an appointment by E-mail or telephone or simply drop by our offices and try and catch us when we are in.

Every year there are a few students who are unable to write a term test at the scheduled time. We will make every effort to accommodate those students who have encountered difficulties that are beyond their control. Students who petition for special consideration for medical reasons MUST use the University of Toronto Student Medical Certificate. Contact Professor Collins for problems with tests and other difficulties related to the administration of this course.

Accessibility Needs:
The University of Toronto is committed to accessibility. If you require accommodations for a disability, or have any accessibility concerns about the course, the classroom or course materials, please contact Accessibility Services as soon as possible:
Students agree that by taking this course all required papers may be subject to submission for textual similarity review to for the detection of plagiarism. All submitted papers will be included as source documents in the reference database solely for the purpose of detecting plagiarism of such papers. The terms that apply to the University's use of the service are described on the web site.


MGY311Y Learning outcomes


The purpose of this course is to show you how science is done in the field of molecular biology. You will learn a certain amount of vocabulary and some facts, but the emphasis will be on how we come to know something, rather than just what we know. We will also discuss what we don't yet know, and how current research is attempting to answer these questions.

By the end of the course we would like you to be able to:


1. Explain, using examples, how the following are important to the function of a cell and organism:

         Nucleic acid structure

         Protein structure

         Macromolecular complexes

         Interactions among proteins, DNA, RNA and small molecules



         DNA Repair


         RNA Processing



2. Interpret data obtained from molecular biology experiments:

        Read the primary literature and write your own interpretations of it.

        Identify the strengths and limitations of individual experimental approaches.

        Appreciate the importance of positive and negative controls.

        Integrate data from multiple experimental approaches to make a stronger conclusion.

        Design experiments to address specific molecular biology questions.



Recommended textbook:

Molecular Biology by Robert F. Weaver, 4th edition, 2008, McGraw Hill.

(The 3rd edition, 2004, is also OK).

There is no required textbook for this course. Students are responsible for material presented and handed out in class. However, in previous years students have found this text to be a very useful reference. Weaver may also serve you double-duty as a textbook for MGY420H next year.


We have also asked Gerstein Library to put copies of the text on the short-term loan shelf.

The text for BIO240/241 may also be a useful resource (Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walter, P. 2007. Molecular Biology of the Cell, 5th ed., Garland Science, New York.) You may want to keep it this year. The 4th edition is also available online via the NCBI website although the format is different than the printed book. This NCBI website is also a good online source for genetics texts.

MGY 311Y Molecular Biology: Outline/Schedule 2012-2013


Location and Time:

Rm 2172, MSB, MWF 9 a.m. (except for the 2 term tests, which will start at 8:30 am).

Term 1: September 10 to December 5, 2012

Introduction to the course and to Molecular Biology (Dr. Rick Collins):

Sept. 10 and Sept 12


I. Nucleic Acids (Dr. Christopher Pearson)

5 lectures: Sept. 14 - Sept. 24

[non-standard DNA structures; repeats, transposable elements, chromosomes]

II. DNA Replication (Dr. Barbara Funnell)

10 lectures: Sep. 26- Oct. 19, except Thanksgiving Oct. 8

[DNA replication in E. coli - initiation, elongation, termination; protein machines; eukaryotic DNA replication; regulation; replicating the ends of chromosomes

III. DNA Repair (Dr. Jim Ingles)

8 lectures: Oct. 22 - Nov. 7

[mutagenesis; repair mechanisms]

Nov. 12: Study Break, no lecture


Term test #1: Wednesday November 14, 2011 at 8:30-10 am (25% of course mark).


IV. Recombination (Dr. Jim Ingles)

9 lectures: Nov. 9 - Dec. 3 (excluding Nov.12 study break and Nov.14 term test)

[Homologous, site-specific, and transpositional recombination in prokaryotes and eukaryotes]



Term 2: January 7 to April 5 , 2013

Essay outline due: Tuesday, Jan. 15, 12:00 noon

V. Transcription (Dr. Jim Ingles)
8 lectures: Jan. 7 - Jan. 23
[mechanisms of transcription - initiation, elongation, termination; initiation complexes in E. coli and eukaryotes; regulation of transcription]

Term test #2: Friday Jan. 25, 2013 at 8:30-10 am (20% of course mark).


VI. RNA Processing (Dr. Rick Collins)

9 lectures: Jan. 28 - Feb. 15

[processing and modification of tRNA and ribosomal RNA precursors; catalytic RNAs; processing of mRNA precursors; non-coding RNAs; RNA editing; RNA silencing; RNA localization]

Reading week: Feb. 18 - Feb. 22


Essays due: Thursday, Feb.28 at 12 noon (25% of final mark). See instructions on the essay webpage for handing in electronic and hard copies and for late penalties.


VII. Translation and Post-translational processing (Dr. Andrew Wilde)
12 lectures: Feb. 25 - Mar. 22
[genetic code(s), tRNA and aminoacyl tRNA synthetases; structure of the ribosome;
protein synthesis - initiation, elongation, termination; regulation of translation;
secretion and targeting; post-translational modification]

VIII. Functional Genomics (Dr. Jim Ingles)

5 lectures: Mar. 25 - Apr. 3
[large-scale approaches to identifying gene functions: microarray, synthetic genetic array, proteomics]

Final exam: during Final Exam period Apr 10 - 30 (30% of final mark)


Grading Summary:
25% Term test 1. Wednesday Nov. 14, 2012
20% Term test 2. Friday Jan. 25, 2013
25% Essay. Feb. 28, 2013
30% Final exam. TBA: April 10- 30, 2013


Students write an individual essay on a scientific topic related to the material covered in the course. The essay assignment is a 3-step process: (1) choose a topic (Nov), (2) submit an outline of the essay (Jan), and (3) complete the essay (due Mar).

Oct-Nov 2012: Topics will be posted on Blackboard
Jan. 15, 2013 (12 noon):
Essay outlines must be approved by this date
Feb. 28, 2013 (12 noon): Essays due

Each instructor will contribute a list of topics from his/her topic area. Each student must choose a different topic. Essays must be no more than 4000 words, which corresponds to about eight typewritten pages. This limit does not include the figures and references.

The essays, which are worth 25% of the final mark in the course, will be graded by qualified graduate students under the supervision of the course lecturers. Your grade will be based on how well you present and argue your case (including style, composition, and spelling) and how well you have researched the subject. Marks will be deducted if the submitted essay does not follow the approved outline. You will be asked to submit a paper copy of your essay for marking, and an electronic file to to facilitate our ability to monitor plagiarism.

Essay topics
We will provide a list of topics, instructions on how to choose a topic, and guidelines for essay preparation on the Blackboard site in Oct-Nov.

Each student must choose an essay topic from the list that we provide. Your choice of topics will usually require some preliminary reading and/or discussion with the instructors. Once you have selected a topic you should request it as soon as possible because each student must write on a different topic and the "best" topics go quickly. We shall keep an updated database of the topics that have been picked.

Essay outline and due date
The next step is to submit a one page outline and a list of references to the appropriate instructor. The references must include some that were published in the past year. The outline must then be approved by the appropriate instructor. The absolute deadline for APPROVAL of outlines is Tuesday, Jan. 15, 2013 at 12 noon.

If you miss this deadline, the penalty is 10% from your essay (ie 3% from your final course mark). In order to meet this deadline, you must submit your outline to the instructor at least several days ahead of time - you should allow at least one week! You should NOT expect instantaneous approval.

The instructor can approve your outline in writing or by email. You will then upload a copy into Blackboard under Assignments. Keep all email or written correspondence with the instructor as your confirmation of approval.

Researching and writing your essay
As soon as your outline is accepted you may begin researching and writing your essay. Detailed guidelines for essay preparation are here, and will also be accessible through Blackboard. We encourage you to talk to the instructor who is assigned to the essay for help and suggestions.
See Essay Guidelines

Essay due date and late penalties
Essays are due before noon on Thursday February 28, 2013. Please hand in the hard copy to the MolGen Office, room 4396, MSB. Make sure you have your name and student number on the essay. Do not email your essay to the instructors or the Department. You will also submit an electronic copy directly to
Late penalties: 10% by Fri Mar. 1, 20% by Mon Mar. 4, 30% by Fri. Mar 8. Essays handed in after Mar.8 will receive a mark of 0%. Note that each 10% from the essay mark is equivalent to 2.5% from final course mark.


(for students, Faculty advisers and TA markers)


This essay accounts for 25% of the final mark for the course. Each student chooses a topic and prepares a one-page outline that must be approved by a Faculty member by Tuesday February 15, 2013. The essay is due on Thursday Feb.28, 2013 at 12 noon.

Students should submit:

1) a paper copy of the essay
2) a paper copy of the approved outline
3) paper copies of 2-3 key reference articles
4) an electronic copy of the essay via the website "". The text of the electronic version MUST be identical to that of the paper copy that you hand in (Figures, legends and Reference list do not need to be submitted to Instructions for electronic submission will be posted on Blackboard before the submission deadline.

The hard copies of your essay, outline and references (items 1, 2 and 3 above) must be handed into the MolGen Departmental Office, room 4396, MSB, before 12:00 noon on Feb. 28, 2013. The electronic copy must be submitted to by midnight of the same day.

Overall essay format:

1. The title page must have your name, your student number, the essay title, and the name of the faculty member who approved your outline.

2. The upper limit is 4000 words of text.
This limit includes the abstract but does not include the references, tables or figures. An essay of 4000 words corresponds to about 16 double-spaced pages. The number of figures is not limited but keep it reasonable. You are not obliged to fill the 4000 words. You donít want to try the patience of your TA marker. Sometimes "less is more".

3. Include page numbers on all pages. The text must be double-spaced, in at least 12-point font, and the margins should be 2.5 cm or 1 inch.

4. The essay must be entirely in your own words. Any copying of ideas and/or words without proper referencing is considered plagiarism.

Details of Essay sections:

1. Title page.
This should be on a separate page and should contain the title that need not be identical to the listed topic. Make it short but above all, informative; it should tell the reader what the essay is about. This page should also contain the student's name, number, the course name and number, as well as the associated Faculty member.

2. Abstract.
The abstract should be less than 250 words and should occupy a separate page. It should summarize succinctly what the essay is about, what you are going to argue or what story you are going to tell. It may resemble your outline but should not be identical to it. Your perspective on the topic should have matured considerably since you wrote the outline.

3. Introduction.
This should give the essential background to the topic, a review of the relevant literature. Although the TA readers will have a background in molecular biology and will have taken MGY311 or equivalent, don't assume that they're an expert in your chosen topic. No one minds reading a coherent background even if they know it. It is aggravating to read one that is opaque and too specialized. The introduction needn't be too long, probably not more that 15-20% of the entire essay. At the end of it you should prepare the reader (again!) for what is coming: what you are going to present, what question you're addressing, what thesis you're proposing or what conflict in the literature you're going to explore, as well as what you conclude.

4. The body of the essay.
This would correspond to the "Results" section of a research paper and will be the "meat" of your essay. Here you will examine the data from your literature review that's most relevant to your topic. If you're examining a hypothesis, you'll give the evidence for (and against) it here. If you're tracing the development of a certain body of knowledge, here's where you state how it has arisen. Do not just reiterate statements from published work: show that you understand how a certain piece of data supports a conclusion. Show that you appreciate the limitations of particular experimental approaches. This section should probably comprise about 60% of the essay. Be certain to acknowledge the sources of your information here.

5. Discussion.
This is where you get a chance to "free-wheel" a bit. You can give the pros and cons of a controversy and weigh in on one side or the other. You may speculate on future developments in a field, on its impact in science society, medicine etc. If you have put forward a hypothesis this is where you might suggest experiments to test it and present their expected outcomes. Note: You needn't adhere rigidly to the above three headings. In fact it helps the reader if you break up the main essay segments into smaller segments with frequent informative headings. Make them short and declarative i.e. "Cre resolves dimeric plasmids" rather than "A Study of the role of the Cre Recombinase in the Replication of dimeric P1 Molecules formed during Plasmid replication and General recombination."

6. References and bibliography.
The references you cite go in a list at the end of your essay. You should reference your essay extensively by citing original papers and reviews. Textbooks are good for getting started but we expect you to read the original literature. Proper referencing is crucial to avoid the problem of plagiarism (see special section below). However you must be reasonable. Certain facts are accepted as such and don't need to be referenced (e.g. "DNA is the genetic material"). You need to use some judgment here, otherwise your reference list will be huge. A reference manager program such as EndNote is a good idea; it allows you it download citations directly from PubMed. Choose a journal format that includes titles to list the references in your bibliography. Do NOT cite references as web links.

Choose 2 to 3 key references from this list and supply paper copies to aid your TA in grading your essay.

7. Figures, legends and tables.
Figures can greatly enhance your presentation. Include relevant figures that show the key pieces of data required to support the conclusions that you are going to draw in your essay. Supply a brief legend under each figure: if the published legend is sufficient, you can include it (just be sure to reference it appropriately); alternatively, you can write your own version of the legend if that helps to show that you understand the data. Figures and tables can be interspersed in the text or grouped together at the end of the essay (after the Reference list). If you take a figure from a publication or use a modification of one, reference the source.

The university and we regard plagiarism as a serious offence and its punishments can be severe. Basically plagiarism is equivalent to stealing. It is pretty easy to detect but harder to prove. Sometimes it is innocent; it's simply caused by improper referencing. Other times it involves "cutting and pasting" which is very easy these days. You may think it's harmless ("how could I say it better than they did?) but it is plagiarism. Copying sentences or sections within quotations and with referencing is not plagiarism but it is bad essay writing. You must express things in your own words. There are several references to plagiarism on the handouts and on many U of T websites (example). The university has a website dedicated to it (How not to plagiarize).

The University has purchased a license to use "", a web-based submission program that is used by many universities in Canada and the US to deter and detect plagiarism. will scan your essays for us for evidence of plagiarism.

Below you will find several useful links at U of T that will help you to research, organize and write your essay.


How will essay be graded?
The TAs will apportion your grade roughly according to the following scheme:

Content: ~30%:
This includes how well you covered the topic, did you include all the relevant references or did you include too many irrelevant ones?

Interpretation ~30%:
Did you interpret the data correctly? Did you convey a clear understanding of the papers you cited? Did you argue your point of view effectively?

Was your presentation convincing? Was it written in a straightforward transparent style? You would be advised to visit the websites on U of T and read the handout material to see some of the common flaws in student (and Faculty) writing. See, for example,

Physical presentation~10%:
This includes figures, diagrams as well as things like spelling, grammar, including page numbers, proper formatting of references, etc. Of course you should spell-check but note that the grammar checks in Word are not always reliable.

This is very hard to quantify but easy to recognize. Did you come up with any novel insights, interpretations, hypotheses or experiments? This is what might well distinguish a B+, A- effort from an A+.