Brock University - Department of Chemistry

Chemistry / Biotechnology 2P63 - Introduction to Biophysical Chemistry

Instructor:      H. L. Gordon
Office:           E220
e_mail:          gordonh@abacus.ac.brocku.ca

Office hours: I am regularly in my office between 9am-5pm weekdays. Students are welcome to drop by.
To ensure that a meeting however, please e-mail me at the above address to arrange a time.

LECTURE TIMES: Monday, Wednesday, Friday 11:30am -12:30 pm ED207

1. REQUIRED TEXTBOOK

“Physical Chemistry: Principles and Applications in Biological Sciences.”, 3rd edition,
I. Tinoco Jr., K Sauer and J.C. Wang, Prentice-Hall, New Jersey, 1995.

2. INTRODUCTION AND COURSE REQUIREMENTS

A. General
CHEM/BTEC 2P63 is an introductory course on topics in physical chemistry as applied to
the life sciences. This course is intended to provide students with a basis for understanding many
of the biophysical processes which occur in nature. Many of the topics covered (free energy;
equilibrium; kinetics) are important concepts used in subsequent courses in biology, chemistry,
and biotechnology.

The prerequisites for CHEM/BTEC 2P63are: CHEM 180/181 or CHEM 190/191, and
MATH 1P93/1P94 or MATH 1P97/1P98. A student must have passed the prerequisite courses
or their equivalents prior to taking CHEM/BTEC 2P63. Students who have the prerequisite
courses have demonstrated some mastery of material and skills necessary for successfully
completing CHEM/BTEC 2P63. To facilitate true understanding of the subject the lectures will
have a reasonable mathematical approach. Students who do not have the prerequisite courses are
severely disadvantaging themselves. Their lack of background in chemistry and/or math slows
down the class and therefore proves a disservice for other students registered in the course.
Therefore students who do not have the prerequisites as outlined above will be deregistered if
they do not voluntarily withdraw from the course or switch to an audit status.

Students enrolled in CHEM/BTEC 2P63 are reminded that provisions are available
through student services for consideration for those having documented special needs. Students
requiring special considerations should make arrangements in advance with student services to
inform the instructor as to what appropriate considerations are required.

B. Assignments
There will be a total of 8-10 assignments in class. The problems will vary with the material
being covered. These are intended to enhance your understanding of the course and to help you
develop problem-solving and critical thinking skills.

C. Examinations
There will be two midterm tests and a three hour final examination. Both mid-terms will
be held during a regularly scheduled class time (Monday, Oct. 16 and Monday, Nov. 13). There
will be NO makeup tests for missed midterms. Should a student miss a midterm for a valid
reason (see below), their mark on the remaining midterm will be used for the entire 20% assigned
to tests (see marking scheme below). Both lecture and laboratory material will be covered on
tests and exams. Questions asked in the mid-term and final examinations will cover topics from
the beginning of term.

3. MARKING SCHEME

      Tests                                                         20%
      Assignments (8-10 in total)                        20%
      Labs (3 informal: 10%, 3 formal: 15%)      25%
      Completed Lab Notebook                          5%
      Final Examination                                      30%

This marking scheme is subject to the DEPARTMENT POLICY on final examinations:
students must achieve a mark of at least 30% on the final exam in order to receive a passing
grade in the course. Furthermore, completion of all laboratories and submission of a completed
lab notebook is also required to obtain a passing grade in the course.

The final examination will cover all topics covered during the semester, including
principles introduced in the laboratory experiments. Copies of previous final examination
papers are available from the Reserve Section of the Library.

4. MISSED LABS OR TESTS

Labs start the first week of classes.

A student may miss a lab or test ONLY as a result of illness, a death in the immediate
family, or a conflict with another course. The Department of Chemistry has a form that must be
filled out by a physician in cases of illness. Students may get this form from the instructor or
from the main chemistry office. No other documentation will be accepted as proof of illness.
In the event of a conflict with another course, students must provide the instructor with the name
of the course and the nature of the conflict prior to the event. A laboratory that is missed for the
given allowable reasons can be rescheduled; a lab missed for any other reason is automatically
assigned a grade of zero. A missed lab should be made up at another time (see below for how to
reschedule a missed lab). See above for policy on missed midterm tests. Final examinations are
administered by the Registrar's Office and exam regulations are available elsewhere. Please note
that it is the student's responsibility to read the FINAL exam timetable and be in the right place at
the right time for exams. Missing an exam as a result of mis-reading scheduling is NOT an
acceptable excuse.

5. PENALTY FOR LATE WORK

It is the Chemistry Department policy that late work is penalized 10% for each day that
the assignment (or lab) is late, with no credit given after 5 days, OR after the material has been
marked and returned to students, whichever comes first.

Assignments are deemed to be late if not received by 8:30 AM the day after the due date.
Remember that all of the labs must be completed and handed in to pass the course; therefore it is
better to hand them in late rather than not handing them in at all.

6. CHEM/BTEC 2P63 LECTURE SCHEDULE

Chapter numbers refer to the text by Tinoco et al. (Third Edition). Not all material will be
covered in every chapter listed.

Sept 11-15     Brief review of mathematical techniques - linear regression; differential and
                       integral calculus; logarithms; Beer’s Law
Sept 18-27     Chapter 2 The First Law (1.5 weeks)
Oct 2-6         Chapter 3 The Second Law (1 week)
Oct 9              Thanksgiving - no class
Oct 11-20      Chapter 4 Free Energy and Chemical Equilibrium (1.5 weeks)
Oct 16            Mid-term Test I
Oct 25-Nov 3  Chapter 5 Free Energy and Physical Equilibrium (1.5 weeks)
Nov 6-10       Chapter 6 Molecular Motion (1 week)
Nov 13           Mid-term Test II
Nov 15-22      Chapter 7 Kinetics (1 week)
Nov 27-Dec 4  Chapter 8 Enzyme Kinetics (1 week)

LABORATORY INFORMATION

TABLE OF CONTENTS

                        1.      Laboratory Demonstrators
                        2.      General Lab Information
                        3.      Marking Scheme
                        4.      Acceptable Excuses for Missed Labs
                        5.      Penalties for Late Work
                        6.      Lab Schedule
____________________________________________________________________________
1. LABORATORY DEMONSTRATORS

Senior Lab Demonstrator: Donna Vukmanic E222
e-mail: dvukman@chemiris.labs.BrockU.Ca

Names of other laboratory demonstrators will be given during the first two laboratory sessions.

Laboratory sections:          Tuesday 9:30pm-12:30pm
                                         Wednesday 2:30pm-5:30pm
                                         Thursday 2:30pm-5:30pm

2. GENERAL LAB INFORMATION

Location: E303

Lab Manual: Lab Manuals will be available from the bookstore at a nominal fee.

Lab Coat: Required for all labs. Lab coats can be purchased from the bookstore.

Lab Notebook: All data collected in labs must be entered into a hard cover notebook with numbered pages.

Safety Glasses: Required for all labs. These can be purchased at the bookstore.

Start Date: The first laboratory session will be held during the first week of classes.

Students will attend laboratories once a week, as per the schedule given during the first
week of labs. Except for the first experiment, all experiments are done on a rotational basis and
will be done by students working in pairs. There is one common experiment and a total of five
rotating experiments, some of which will take 2 weeks to complete. Formal lab reports are
required for three of the six experiments and are due two weeks after completion of the
experiment. An example of a formal lab will be described at lab check-in during the first week.
For the remaining labs all data, calculations and write-ups should be recorded in your lab book.
Photocopy of the completed lab report should be handed in one week after completion of the lab
into the report box located across the hall from E222 and labeled with appropriate course and
demonstrator name. Completed lab books must be submitted at the end of the course in order to
obtain a passing grade in the course. In addition, ALL labs must be completed and ALL lab
reports must be handed in to obtain a passing grade in the course.

3. LAB MARKING SCHEME (30% of course mark)

                          3 Informal Labs         10%
                          3 Formal Labs           15%
                          Completed Lab Notebook 5%

Completion of all laboratories and submission of a completed lab notebook is required to
obtain a passing grade in the course.

4. MISSED LABS

A student may miss a lab ONLY as a result of illness or a death in the immediate family.
In cases of illness a doctor's certificate will be required as proof. In case of the missed lab
arrangements must be made with the senior demonstrator to make up the lab at another time.
Because of the rotating schedule of labs (see §6 below) it is NOT possible for students to drop in
to other lab sections to make up missed labs! Being late for the lab without prior explanation
will be regarded as a missed lab.

5. PENALTY FOR LATE WORK

It is the Chemistry Department policy that late work is penalized 10% for each day that
the lab is late. Remember that all of the labs must be completed and handed in to pass the course,
therefore it is better to hand them in late rather than not handing them in at all.

6. CHEM/BTEC 2P63 LAB SCHEDULE

All labs are done by partners, in rotation. The experiments provide practical experience to
complement many of the topics covered in the lectures.

The lab manual contains sufficient information for each student to be able to successfully
complete the lab, analyze the data and prepare the lab report. For each experiment the lab
manual, as well as the additional references which are given in the lab manual, must be read
BEFORE coming to the lab. You will be provided with a list of reference material that is placed
on reserve in James A.Gibson Library. In addition, the introduction and a point form procedure
must be done before each lab, and checked by the demonstrator. Labs run for three hours, and it
is expected that students will complete all required work within this period. Please
note that for experiments done in pairs, each partner must complete his/her own lab report for
submission to the demonstrator. Plagiarism will NOT be tolerated.

Week 1:   Check-in.
               Discussion of safe lab practices.
              Analytical techniques.
              Overview of experiments, lab notebooks, general lab reports and formal reports.
              Math review: Algebra assignment 1.

Week 2: Part 1, Experiment 1: Adsorption of Acetic Acid by Activated Charcoal

Week 3: Part 2, Experiment 1: Analysis of Amount of Acetic Acid Adsorbed by Charcoal.

Weeks 4-12:
The following laboratory experiments to be done in rotation:

2. Probing Protein Denaturation by Monitoring of Activity and Fluorescence (2 weeks).
3. Protein Extraction and SDS-PAGE Electrophoresis (2 weeks).*
4. Protein Isolation and Size Exclusion Chromatography (2 weeks).
5. Kinetics of the Reaction Between Urease and Urea (1 week).*
6. Dye-Protein Binding (1 week).*

* These experiments require formal lab reports (see §2-3 above).

Students are expected to leave their lab equipment in good order at the end of the day, ready for
the next set of students to use.

University Page Faculty Page Chemistry Page

This page is: http://chemiris.labs.brocku.ca/~chemweb/courses/chem263/chem263.html