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COURSE DESCRIPTION
The field of molecular biology is rapidly evolving and with it comes a greater understanding of the central
dogma, DNA makes RNA makes protein. The primary aim of this course is to examine the regulatory
mechanisms that control the production of RNA from DNA (Transcription) and protein from RNA
(Translation). More broadly, this course looks at methods of gene regulation in both prokaryotic and
eukaryotic systems.
Topics include prokaryotic and eukaryotic transcription, RNA splicing/processing/stability/localization,
translation, epigenetics and regulatory RNA, new techniques used to modulate gene expression.
LEARNING OUTCOMES
By the end of this course student will be able to:
1. Discuss the processes governing gene transcription in prokaryotic and eukaryotic cells.
2. Describe the mechanisms that govern chromatin structure and explain the role of chromatin in
gene regulation.
3. Discuss the topics of epigenetics and epigenomics.
4. Describe the processing and translation of RNA and explain the role of non-coding RNA in gene
regulation.
5. Discuss cutting edge methods used to study various aspects of gene regulation covered in
lecture.
6. Read primary scientific literature at sufficient depth to provide an accurate summary and
comment on the overall conclusion and importance of the work.
7. Apply concepts and knowledge about gene regulation and scientific methods to interpret novel
datasets.
COURSE MATERIAL
1. Textbook: Fundamental Molecular Biology, 2nd Edition by Lizabeth A. Allison.
ON RESERVE at Taylor Library. Much of the lecture material is derived from this text. This text
will be very useful for reinforcing concepts discussed in lecture. Recommended to purchase.
2. Textbook: Molecular Biology of the Gene, 7th edition, by James D. Watson.
ON RESERVE at Taylor Library. Some subject and figures covered in lecture are derived from
this text and not present in Allison.
3. Lecture slides available on OWL. I will make these slides available usually just before the lecture
time.
4. Other reading material from scientific literature will be suggested for selected topics that are not
covered in text books
5. Students should check OWL on a regular basis for news and updates. This is the primary method
by which information will be disseminated to all students in the class. Students are responsible for
checking OWL on a regular basis.
EVALUATION
METHODS:
1. Text reading prior to attending class, as indicated on schedule and in lecture.
This course is challenging and fast paced. To be successful, you must attend all lectures and read
the assigned material BEFORE and after each lecture. Do not fall behind!
2. OWL FORUM
If after the lecture and after you study, you do not understand something, please consult the OWL
forum, where your question might already have been addressed. If your question is not addressed
in the forum, then post your own question there. Students should feel free to answer questions in
the forum that are posted by your classmates. The forum will also be monitored by the instructors.
3. Tutorials
The goals of the tutorials will be to review lecture material and learn about current methods in
gene regulation research. The tutorial will start with a quiz and a review of the previous quiz. This
will be followed by a 20-30 min session in which you will learn about an important method in gene
regulation research. The methods discussed will be directly relevant to the annotation
assignments.
a. Quizzes (20%): 9 quizzes of 15 min. (multiple choice or short answers) at the beginning of
each tutorial – lowest 1 dropped. No make-up quizzes. The purpose of the quizzes will be
to review lecture material from the previous week.
b. Annotations (15%): 3 in total – see schedule for due dates. Each student will bring an
annotation of a primary research paper, which will be posted on OWL 1-2 weeks prior to
the deadline.
4. Mid-term and Final Exam
a. Both with cheat-sheet (one side of an 8.5” X 11” page, with the student’s name, to be handed
along with the exam).
b. Mid-term will cover lectures 1-12. Combined multiple choice and short answer. With proper
documentation, the grade for the mid-term will be reported to the final. If a student has prior
knowledge of a conflict with the scheduled mid-term test, they must inform the instructor
prior to the date of the term test. There will be NO make-up mid-term.
c. The final exam will be scheduled by the registrar during the regular exam period. It will be
cumulative, covering material from the entire year. It will combine multiple choice and short
answer and will contain an annotation style question involving a novel dataset.
d. Statement on the Use of Electronic Devices. No electronic devices (including but not
limited to laptop computers, cell phones, iPods, etc.) will be allowed during examinations
unless expressly authorized by the instructor.
ACCOMIDATION AND ACCESSIBILITY
If you are unable to meet a course requirement due to illness or other serious circumstances, you
must provide valid medical or supporting documentation to the Academic Counselling Office of your
home faculty as soon as possible. If you are a Science student, the Academic Counselling Office of
the Faculty of Science is located in WSC 140, and can be contacted at scibmsac@uwo.ca. For further
information, please consult the university’s medical illness policy at:
http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_medical.pdf.
If you miss the Final Exam, please contact your faculty’s Academic Counselling Office as soon as you
are able to do so. They will assess your eligibility to write the Special Exam (the name given by the
university to a makeup Final Exam). You may also be eligible to write the Special Exam if you are in a
“Multiple Exam Situation”. See http://www.registrar.uwo.ca/examinations/exam_schedule.html.
ACADEMIC POLICIES.
The website for Registrarial Services is http://www.registrar.uwo.ca.
In accordance with policy, http://www.uwo.ca/its/identity/activatenonstudent.html, the centrally
administered e-mail account provided to students will be considered the individual’s official university
e-mail address. It is the responsibility of the account holder to ensure that e-mail received from the
University at his/her official university address is attended to in a timely manner.
Scholastic offences are taken seriously and students are directed to read the appropriate policy,
specifically, the definition of what constitutes a Scholastic Offence, at this website:
http://www.uwo.ca/univsec/pdf/academic_policies/appeals/scholastic_discipline_undergrad.pdf
Computer-marked, multiple-choice tests and exams may be subject to submission for similarity review
by software that will check for unusual coincidences in answer patterns that may indicate cheating.
We may use iClickers for informal assessment in class. Students’ privacy will be protected with
respect to data gathered from the responses, that the data gathered using the devices will not be
used for research purposes without their consent, and that they cannot be used by anyone but the
student.
SUPPORT SERVICES
Please contact the course instructor if you require lecture or printed material in an alternate format or
if any other arrangements can make this course more accessible to you. You may also wish to contact
Services for Students with Disabilities (SSD) at 661-2111 ext. 82147 if you have questions regarding
accommodation.
The policy on Accommodation for Students with Disabilities can be found here:
http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_disabilities.pdf
The policy on Accommodation for Religious Holidays can be found here:
http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_religious.pdf
Learning-skills counsellors at the Student Development Centre ( http://www.sdc.uwo.ca ) are ready to
help you improve your learning skills. They offer presentations on strategies for improving time
management, multiple-choice exam preparation/writing, textbook reading, and more. Individual
support is offered throughout the Fall/Winter terms in the drop-in Learning Help Centre, and year-
round through individual counselling.
Students who are in emotional/mental distress should refer to Mental Health@Western (
http://www.health.uwo.ca/mental_health ) for a complete list of options about how to obtain help.
Course Schedule (subject to change)
Book Tutorial
Week Lecture Topic
Chap. Papers on owl
Lec1: Introduction: The Central Dogma
1 No tutorial
Lec2: Genome Organization – DNA to 2, 3, 5
Week of Sept 11
RNA
Lec3: Transcription in Bacteria 1 10 Introduction
2
Lec4: Transcription in Bacteria 2 METHODS: RNA
Week of Sept 18
detection
Lec5: Transcription in Bacteria 3 10 Quiz 1
3
Lec6: Transcription in Bacteria 4 METHOD: Protein
Week of Sept 25
detection
Lec9: Transcription in Eukaryotes 1 11 Quiz 2
4
Lec10: Transcription in Eukaryotes 2 METHOD: RNA and
Week of Oct 2
protein localization
Annotation 1 due Wed Oct 4 in
lecture
5 STUDY BREAK
Week of Oct 9
Lec11: Transcription in Eukaryotes 3 11 Quiz 3
6
Lec12: Transcription in Eukaryotes 4 METHOD: Protein-
Week of Oct 16
DNA interactions
Oct 21 MID-TERM – 9:30-12:30 AHB 1R40
Lec13: Epigenetics and chromatin 1 12 Review midterm
7
Lec14: Epigenetics and chromatin 2 METHOD: Protein-
Week of Oct 23
DNA interactions
Lec15: Epigenetics and chromatin 3 12 Quiz 4
Lec16: Epigenetics and chromatin 4 METHOD: Protein-
8
DNA interactions
Week of Oct 30
Annotation 2 due Wed Nov 1 in
lecture
Lec17: RNA 1 13 Quiz 5
9
Lec18: RNA 2 METHOD: Protein-
Week of Nov 6
RNA interactions
Lec19: RNA 3 13 Quiz 6
10
Lec20: RNA 4 METHOD: Protein-
Week of Nov 13
RNA interactions
Lec21: Translation 1 14 Quiz 7
11
Lec22: Translation 2 METHOD: Protein-
Week of Nov 20
RNA interactions
12 Lec21/22 – to be determined No tutorial
Week of Nov 27
Lec23: Translation 3 14 Quiz 8
Lec24: Translation 4 Exam Review
13
Week of Dec 4
Annotation 3 due Wed Nov 22 in
lecture