BIOLOGY DEPARTMENT T U

BIOLOGY DEPARTMENT
TRENT UNIVERSITY
BIOL3080H: Molecular Biology
2014-15 FA
Peterborough
Instructor:
Prof. Janet Yee
Campus: Peterborough
Email:
[email protected]
Office Location: CSB E110
Telephone:
x7048
Office Hours: Mondays 5 – 6 PM
or by appointment
Secretary: Sandy Sisson
Office Location: DNA D102
Email: [email protected]
Teaching Assistants:
Kathleen Horlock-Roberts
Guillem Dayer
Andressa Lacerda
Kelly Nori
TBA
Laboratory Demonstrator: Smolly Coulson
Email:
[email protected]
[email protected]
[email protected]
[email protected]
TBA
[email protected]
Telephone: x7424
Course Description:
Molecular biology attempts to explain the heredity and functioning of cells in terms of the molecules
that control them. Although these processes appear complex and diverse upon initial examination,
closer analyses reveal, “an astonishing elegance and economy in the living cell and a gratifying unity
in the principles by which cells function.”1 We will explore several concepts in molecular biology
with emphasis on the structure, function, and cellular synthesis of DNA and RNA. Techniques in
recombinant DNA technology as well as their applications in biomedical, forensic, and
pharmaceutical research will also be discussed. Basic techniques in molecular biology as well as
scientific calculations will be introduced in the laboratory portion of the course.
Course Pre-requisites:
7.5 university credits including BIOL 1030H (103H), 2050H (205H), either CHEM 1000H and
1010H or 100. Excludes BIOL 206H and 308H.
Required Texts:
Molecular Biology of the Cell, 5th edition by Bruce Alberts et al. This textbook will also be used
in BIOL 438H: Advanced Molecular Biology.
LearningSystem/Blackboard:
Students must be officially registered in this course in order to access the BIOL3080H website in
MyLearning.
1
Bruce Alberts et al., 1983, preface in Molecular Biology of the Cell, 1st edition, Garland Science, New York.
Course Format:
Please check https://scheduler.trentu.ca/AcademicTimetable/Peterborough/FallWinter/ to confirm
times and locations.
Type
Lectures
Laboratories
Day
Monday
Tuesday
Alternate Tuesdays
Time
4:00 – 4:50 PM
4:00 – 4:50 PM
9 – 12 AM OR
1 – 4 PM
Location
GCS 114
GCS 114
DNA D202
DNA D202
Learning Outcomes/Objectives/Goals/Expectations: I have developed the course to address
several learning outcomes. By the end of the course a successful student should:
1. Understand and be able to draw the structures of DNA and RNA
2. Know the steps involved in DNA replication and the enzymes involved in this process
3. Understand the fundamentals of key molecular biology techniques including PCR,
restriction enzymes, plasmids, nucleic acid hybridizations, and DNA sequencing.
4. Learn the basic outline of transcription and translation
5. Gain an understanding of the regulation of the cell cycle and the role of this process in
carcinogenesis.
Course Evaluation:
Normally at least 25% of the grade in an undergraduate half-credit course offered in the
Fall/Winter academic session must be determined and made available by the final date for
withdrawal. Fall 2014, final date for withdrawal is November 4, 2014.
Type of Assignment
Test 1
Test 2
iClicker
Labs
Final Exam#
Total
Weighting
21%
21%
2%
22%
34%
100%
Due Date
Mon., Sept. 29
Mon., Nov. 10
Throughout term
*See below
Dec. 5 – 20
*Lab assignments consists of answers to questions relevant to each lab and they are due at the
beginning of the NEXT lab (i.e. the assignment for lab 2 is due at the beginning of lab 3). The
exception to this is lab 6, where the student will work on the assignment during the lab period so
that it would be due at the end of lab 6. See Lab schedule (p. 3) for lab dates.
Participation is mandatory for all labs scheduled for each section, and attendance will be
recorded during each lab period.
**Late Penalty: 5% will be deducted from the grade of a lab assignment for each day it is
submitted past the due date**
#You must be prepare to write the exam at any time and date during the exam period. There will be
no change of the final exam date to accommodate travel plans.
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Biology 3080H Class & Lab Schedule 2014
A tentative schedule of lecture topics is listed below. Although I will try to follow the order of topics as
given, there may be changes to the pacing of the lectures. For this reason, it is important for you to attend all
classes and log on to the learningSystem/Blackboard regularly for updates to the lecture schedule and other
important announcements.
Date
Day
Blackboard file
Lecture topic
Sept. 08
Mon.
DNA & RNA
structure
Structure and properties of
DNA and RNA;
complementary basepairing
09 Tues.
“
"
15 Mon.
DNA replication
16 Tues.
“
22 Mon.
PCR
23 Tues.
Telomeres
29 Mon.
30 Tues.
Oct. 06 Mon.
PCR
Plasmids
07 Tues.
Restriction
enzymes
13 Mon.
Thanksgiving
14 Tues.
Restriction
enzyme mapping
20 - 24
The phosphodiester bond;
leading & lagging strand
DNA synthesis
DNA primase; helicase; SSB
proteins; topoisomerase I &
II; other proteins at a DNA
replication fork
The 3 steps of a PCR cycle;
PCR primers; gel
electrophoresis
DNA replication at ends of
linear chromosomes;
telomerase
Test 1
RT-PCR and its application;
the use of PCR in DNA
fingerprinting
Structure and properties of
plasmids; “stringent” and
“relaxed” replication;
bacterial conjugation,
techniques for bacterial
transformation
Restriction and modification
systems in bacteria; types of
DNA ends generated by R.E.
digests; splicing of compatible
DNA ends
No Class
Construction of maps
containing R.E. sites on linear
and circular DNA molecules
by using data from R.E.
digestions
Lab
cycle
Lab (Tues.)
I
Lab 1:
Use of
micropipettors
& lab notebook
II
"
I
Lab 2:
PCR/agarose gel
II
"
I
Lab 3
Bacterial
transformation
II
"
Reading week
3
Biology 3080H Class & Lab Schedule 2014 Cont’d
Date
Day
Blackboard file
27 Mon.
28 Tues.
Recombinant
DNA I
Nov. 03 Mon.
Recombinant
DNA II
04 Tues.
"
10 Mon.
Lecture topic
I
Lab 4:
Isolation of
plasmid DNA
II
"
I
Lab 5:
Restriction
enzyme
digestions
II
"
I
Lab 6:
Scientific
calculations
II
"
Test 2
Transcription
Transcription in prokaryotes
and eukaryotes
17 Mon.
Transcription &
Translation
"
18 Tues.
Translation
24 Mon.
Cell cycle
Dec. 01 Mon. Cell cycle/Cancer
02 Tues.
Lab (Tues.)
Return of test 1 & review of
answers
Nucleic acids hybridizations;
radioactive and nonradioactive labeling of DNA;
Southern and Northern blots;
in situ hybridization
Genomic and cDNA libraries;
BAC cloning vectors;
screening DNA libraries;
Steps in DNA sequencing;
automated DNA sequencing;
ID of ORFs
11 Tues.
25 Tues.
Lab
cycle
Cancer
Translation initiation in
prokaryotes and eukaryotes
Return of test 2 & review of
answers
Cell cycle stages &
checkpoints; cdks & cyclins
Oncogenes, tumor suppressor
genes, role of viruses
Angiogenesis; metastasis;
molecular basis of cervical &
colon cancers
Exam period: Fri., Dec. 5 to Sat., Dec. 20, 2014
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University Policies
Academic Integrity:
Academic dishonesty, which includes plagiarism and cheating, is an extremely serious academic
offence and carries penalties varying from failure on an assignment to expulsion from the
University. Definitions, penalties, and procedures for dealing with plagiarism and cheating are set
out in Trent University’s Academic Integrity Policy. You have a responsibility to educate yourself –
unfamiliarity with the policy is not an excuse. You are strongly encouraged to visit Trent’s
Academic Integrity website to learn more: www.trentu.ca/academicintegrity.
Access to Instruction:
It is Trent University's intent to create an inclusive learning environment. If a student has
a disability and/or health consideration and feels that he/she may need accommodations
to succeed in this course, the student should contact the Student Accessibility Services
Office (SAS), (BH Suite 132, 705-748-1281 or email [email protected]).
For Trent University - Oshawa Student Accessibility Services Office contact 905-435-5102
ext. 5024 or email [email protected] . Complete text can be found under Access to
Instruction in the Academic Calendar.
Clickers (Personal Response Systems):
As clicker records are used in this course to compute a portion of course grades, the use of a clicker
other than your own is an academic offence. In lecture or tutorial, possession of more than one
clicker, or that of another student, may be interpreted as intent to commit an academic offense.
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