CHEMISTRY 674

Structural and Physical Biochemistry

Fall 2007
J. C. Dabrowiak

Chemistry 674, Structural and Physical Biochemistry, is the graduate version of

CHE 474. CHE 674 utilizes the syllabus for CHE 474, which specifies, lecture topics,
due dates for homework assignments, exam dates, course policies, etc. Students taking
CHE 674 will be graded on a separate “graduate” grading scale using the exam and
homework assignments weightings described in the syllabus for CHE 474.

1. The three “hourly exams” and the final exam for CHE 674 have a degree of difficulty
appropriate for the graduate student with interests in biochemistry. When compared to
CHE 474, exams for CHE 674 will have additional questions with enhanced degrees of
difficulty.

2. For students in CHE 674, the initial homework assignments (HW-1-3) will contain
more demanding concepts and structures than the corresponding assignments for CHE
474.

3. For students in CHE 674, the “Mini-Project” (HW-4) has equally weighted oral and
written components. The oral component of HW-4 is a 15 minute presentation on the
structure and function of an important biochemical system, the nature of which was
previously agreed on through consultation with the instructor. The oral presentation must
include slides or other visual graphics created by editing an existing PDB file of the
system being discussed using a molecular modeling program. The written component of
HW-4 is a scientific report following the detailed format given in the handout for HW-4.
Course Organization: Structural and Physical Biochemistry, CHE 474, is composed of
four parts, lecture, practice problems, exams, and homework assignments.

Lecture: The lecture material in CHE 474 is collected from the texts, T, E, B, and M,
selected research articles, and other publications. Since the early part of the course
applies basic principles learned in general chemistry to problem solving in biochemistry,
it is important to read and understand appropriate sections in E. As the course progresses,
more emphasis is placed on the physical and structural aspects of biological systems, as
discussed mainly in T (some from B, and M), and detailed chemical kinetic analyses, as
found in T. The lecture material for the final portion of the course, which covers basic
quantum mechanics and absorption spectroscopy, is primarily derived from T.
For the lecture portion of the course, students are expected to take detailed notes
and review them after each lecture. When additional information is required or if a point
made in lecture is not clear, students are expected to seek information from the required
and resource texts as well as from other sources.
It is University policy that cell phones or other electronic devices not be audible
and disturb the lecture environment in any way.

Practice Problems: CHE 474 has an extensive series of “practice problems”, which are
designed to prepare the student for the exams in the course. A paper copy of the problems
(questions) is provided to the student and the solutions to the problems are posted on the
website for the course. A good strategy for working out the solution to a practice problem
is to read the lecture notes that apply and, if necessary, consult appropriate sections in
one or more of the above texts. If after doing so, the approach to solving the problem is
not obvious, consult the solution that is posted on the website. Since an exam question
will not be identical to a practice problem, understanding the scientific logic behind the
setup of a solution is more important than memorizing the solution to a specific problem.
Working out the solutions to practice problems should be started early and it should be
continuous and on-going throughout the course. Saving this task for the night before the
exam is not a good way to obtain a high grade on the exam. No points are allotted for
solving the practice problem sets in CHE 474.
As outlined above, the practice problems are designed to help the student prepare
for the exams in the course. Consulting “hard copies” or electronic versions of the
solutions to the practice problems during exams is academic dishonesty and is strictly
forbidden.

Examinations: Three exams, each weighted 16% of the final grade, will be given on the
dates and time (9:30 AM to 10:50 AM), indicated in the syllabus. These exams, referred
to as “hourly” exams, cover the material for the various parts of the course, Exam I
covers material for Part I, Exam II/Part II and Exam III/Part III. Typically, each hourly
exam consists 7-9 questions with nearly all questions requiring a numerical solution (use
of a calculator). The final exam, which is given on the date and time set by the
University, is comprehensive (covers Parts I-III), and accounts for 30% of the grade in
CHE 474. The final exam generally consists of 9-11 questions with nearly all questions
requiring a numerical solution (use of a calculator). Usually, all of the exams given in
CHE 474 have an attached page that gives formulas, relationships, and other data that are

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important for answering questions on the exam. A full set of exams from the previous
year along with solutions can be found on the website for the course.
During exams, cell phones must be hidden from view and they must not be
auditable during the exam. Under no circumstances is a cell phone to be used as a
calculator during the exam.

Homework Assignments: There are 4 homework assignments in CHE 474 which are
worth 22% of the total grade in the course. For the first assignments, HW-1, HW-2, and
HW-3, each student is given his or her own structure which must be constructed,
manipulated and/or analyzed using the molecular modeling program, HyperChem. This
program can be accessed from computers located in the Learning Center (LC), room 0-
222 of CST. Doing the homework assignments requires that the student reserve one 2
hour block of time, on Tuesday or Thursday of a given week, between the hours of 11
AM and 9 PM in the LC. The sign up list for possible times is passed out at the beginning
of lecture on Tuesday of every week. Note that signing up for a specific time means that
you are expected to be there for that time. If for any reason you cannot make the
scheduled time, it is your responsibility to notify the TA’s in the course as soon as you
know that you cannot make the scheduled time so that, if necessary, the time can be
reassigned. Failure to do so will result in loss of 10% of the grade for the assignment.
The e-mail addresses for the TAs in the course are: Corey Centerwall,
[email protected] and Ben Lundgren, [email protected].
The material submitted for grading for HW-1-3 consists of images of molecules
or structures built/analyzed using HyperChem which are stored on an electronic storage
device, e.g., a diskette, CD, or USB Flash Drive. The student is responsible for providing
the storage device for this purpose which, after submitting to the TA on duty in the LC,
will be in the hands of the grader for about one week during the grading period. Due
dates for homework assignments HW-1, HW-2, and HW-3 expire at 9 PM on the
indicated date stated in the syllabus. The final homework assignment to be turned in for
grading, HW-4, the “Mini-Project”, consists of a written report on an assigned topic with
imbedded figures created using HyperChem. The due date and time for the Mini-Project
is, Thursday November 15, at 9 PM.
The grading scale for "on time" submissions for all homework assignments is 0 to
100%. If the student fails to submit the homework assignment on time, the assignment
will be considered, “late” and the grading scale 0-75% will be applied. Assignments
submitted more than one week after the due date (the 9 PM deadline applies) will be
considered a “missed assignment” and receive a zero score. A student who has missed
the deadline for a homework assignment, but who has a valid medical excuse and has
promptly provided documentation related to the excuse, will be subject to the grading
policy stated above but the 25% penalty for the “late” period will be waived. The
weightings for the homework assignments in the course are, HW1-3 (4% for each), HW4,
the Mini-Project, (10%).

Examination Policies: The dates and times (9:30 AM to 10:50 AM) for the three hourly
exams and the final exam are as indicated in the syllabus. Except for the final exam there
is no possibility to make up an exam. A student with a valid medical excuse or a valid
student-athlete excuse, who has missed one hourly exam, and who has promptly provided

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documentation related to the excuse, can have the averages of the other two exams used
as the score for the missing exam. A student with a second or third "miss" will receive a
grade of zero for the additional missed hourly exam(s). If a student has a valid medical
excuse or a valid student-athlete excuse for a missed final exam, a comprehensive make
up final exam, 2 hours in length, may be taken for the missing grade. The documentation
pertaining to the excuse must be presented promptly after the missed final exam and
reasonable time must be allotted for preparing the make up final exam.

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 CHE 474 (fall 2007)
Date Day Lecture Subject (1-019 CST, 9:30-10:50 AM)
Aug. 28 Tues. 1. Noncovalent Interactions. pp. 97-100, 497-498, 503-
512. Assign Practice Problem Set 1.Assign HW-1.
Getting Started/Building a Drug Molecule.

30 Thurs. 2. Acid/Base Equilibria. pp 163-165.

Sept. 4 Tues. 3. Buffers/Ionic Strength. p.141.

6 Thurs. 4. 1st Law of Thermodynamics/Hess’s Law. pp 22, 48-50.

Assign Problem Set 2.

11 Tues. 5. 2nd Law of Thermodynamics/Chemical Potential

pp. 122-123.

13 Thurs. 6. Equilibrium Dialysis/Scatchard Equation.

pp. 197-202. HW-1 due. Assign HW-2. Studying the
structure of DNA and RNA.

18 Tues. 7. Free Energy and Biological Systems/Activity.

pp 136-137.

20 Thurs. 8. Problem Solving Session.

25 Tues. 9. Exam I.

27 Thurs. 10. Primary Structure of Nucleic Acids.

pp. 101-106. Assign Practice Problem Set 3.

Oct. 2 Tues. 11. Secondary Structure of Nucleic Acids.

4 Thurs. 12. Supercoiled DNA Structure and Properties.

HW-2 due. Assign HW-3. Studying the structure of
proteins.

9 Tues. 13. Physical Properties of Nucleic Acids

Melting. pp. 643-645, 172-175

11 Thurs. 14. Physical Properties of Nucleic Acids. Chemical

Kinetics/Rate Laws. pp. 315-331,
338-339. Assign Practice Problem Set 4.

16 Tues. 15. Chemical Kinetics Rate Laws.

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 18 Thurs. 16. Chemical Kinetics. HW-3 due. Assign HW-4. Mini
Project.

23 Tues. 17. Chemical Kinetics. Equilibrium and Kinetics. pp 349.

25 Thurs. 18. Chemical Kinetics/Activation Energy pp. 354-357.

30 Tues. 19. Exam II.

Nov. 1 Thurs. 20. Schrodinger Equation/Wave Mechanics. Particle in a

Box. pp. 436 - 463. Assign Practice Problem Set 5.

6 Tues. 21. Particle in a Box/The Hydrogen Atom. pp. 469-476.

8 Thurs. 22. Many Electron Atoms/Molecular Orbitals

pp. 476-484.

13 Tues. 23. Hybridization/Molecular Structure and Molecular

Orbitals pp. 484-491.

15 Thurs. 24. Absorption Spectroscopy. Beer-Lambert Law. pp. 530

- 544. Assign Practice Problem Set 6. HW-4, Mini-
Project Due, 9 PM

20 Tues. 25. Absorption Spectroscopy/Quantitative Determinations.

pp. 544-547.

22 Thurs. Thanksgiving. No Lecture.

27 Tues. 26. Absorption Spectroscopy/Equilibrium.

pp. 548-553.

29 Thurs. 27. Absorption Spectroscopy/Proteins and Nucleic Acids.

Dec. 4 Tues. 28. Exam III.

6 Thurs. 29. Review for Final Exam.

12 Wed. Final Exam, 2:45-4:45 PM

Note: The indicated page numbers refers to text, “T”. Homework assignments are
denoted by “HW”.