Advanced Biochemistry

CHEM 4753

Dr. Paul F. Cook

Department of Chemistry and Biochemistry
University of Oklahoma

ADVANCED BIOCHEMISTRY
CHEM 4753, Spring 2006

Instructor Dr. Paul F. Cook

Phone 325-4581
Email pcook@chemdept.chem.ou.edu
Office PHSC 219A
Lectures MWF 8:30 – 9:20 AM, PHSC 201.
Office Hours MW 1:00 PM - 2:30 PM

Background
It is assumed that all students have a fundamental background in Biochemistry. Students
should try to be conversant with lecture topics prior to the lecture. A subjective portion
of the grade will be de rived from class participation. Additional reading assignments
from the text and the literature will be required.

Lectures will roughly follow the text, and students are required to have their own copy.
Lecture outlines, etc. will be pos ted on the Course Web site for CHEM 4753 at the
following URL address: http://cheminfo.ou.edu/~pfc//classes/index.html

OBJECTIVES

This course will provide a con tinuation of the material presented in CHEM 3653
Introduction to Biochemistry. As a result, the introductory course is a prerequisite. The
course will build on the student's general background in biochemistry, and will consider
topics that are more global with respect to their application to the metabolic pathways.
Thus, the topics of energy generation and u tilization, catalysis and con trol will be
stressed overall.

The class will move at a rapid pace because of the amount of material to be covered, and
thus one should try to stay slightly ahead of the lecture schedule with respect to reading
assignments. Staying ahead will also allow the student to derive most from the lectures.

TEXTBOOK

Biochemistry 3rd Ed., Voet, D. & Voet, J. G., John Wiley & Sons, Inc., New York,
1995. ISBN 0-471-19350-x

Other texts that may also be helpful follow:

Biochemistry, 3rd Ed., Matthews, C. K., van Holde, K. E., & Ahern, K. G.
Addison, Wesley, Longman, Inc., San Francisco, 2000.
Biochemistry, 4th Ed., Zubay, G. Wm. C. Brown Publishers, Dubuque, 1996

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ESTIMATION OF GRADE

Grades will be calculated based on t he student’s performance on a number of

examinations, including quizzes, hourly exams and a final. The final will be cumulative,
i.e. will contain information from the entire course. A summary of examinations and
their value is provided below:

Quizzes and Homework 300

Hourly Exams 300
Final* 200

Total 800

Quizzes may or may not be announced. It is important to have a calculator for quizzes,
but notes or other aids are not permitted. THERE WILL BE ABSOLUTELY NO
MAKE-UPS FOR QUIZZES!

Hourly exam dates and the date of the final exam are provided below. Exams will
include material covered in lecture and from reading assignments. MAKE-UP EXAMS
WILL BE GIVEN ONLY IF THE INSTRUCTOR HAS BEEN NOTIFIED PRIOR
TO THE EXAM AND A PHYSICIAN’S NOTE, ETC. IS PROVIDED!

*The standardized American Chemical Society exam in Biochemistry will be used as

the final exam and will cover material presented in this class and the pre- and co-
requisite courses, CHEM 3653 and CHEM 3753.

In the instance a student’s grade is near a grade cut-off, e.g. A/B, the instructor will take
class participation into account for possible grade adjustments.

CODES AND POLICIES OF BEHAVIOR POLICY

Each student should acquaint her or his self with the Universities' codes, policies, and
procedures involving academic misconduct, grievances, sexual and ethnic harassment,
and discrimination based on physical handicap.

REASONABLE ACCOMMODATION POLICY

Any student in this course who ha s a disability that may prevent her or h im from fully
demonstrating his or her abilities should contact me personally as soon as possible so we
can discuss accommodations necessary to ensure full participation and facilitate your
educational opportunities.

LECTURE TOPICS AND SCHEDULE

Date Topic

Jan. 18 Introduction
20 How to Study Metabolism – Glycolysis & PPP

23 TCA & Gluconeogenesis

25 Fatty Acid Synthesis and β-Oxidation
27 Amino Acids

30 Nucleic Acids
Feb. 1 Thermodynamics - First Law
3 Thermodynamics - Second Law

6 Gibbs Free Energy

8 Chemical Energy - Generation and Storage
10 Redox Reactions

13 Redox Reactions
15 Introduction to Enzymes
17 Review

20 Exam 1

2
 Feb. 22 Practical Considerations
24 Introduction to Kinetics

27 Enzyme Kinetics
Mar. 1 Enzymes - Nomenclature
3 Enzymes - Nomenclature

6 Bireactant Enzymes Reactions

8 Inhibition as a Mechanistic Tool
10 Product Inhibition

13 SPRING BREAK
15 SPRING BREAK
17 SPRING BREAK

20 Dead-End Inhibition
22 pH Dependence of Kinetic Parameters
24 pH Dependence of Kinetic Parameters

27 Origins of Catalysis
29 Review
31 Exam 2

Apr. 3 Origins of Catalysis

5 Origins of Catalysis
7 Enzyme Mechanisms

10 Enzyme Mechanisms
12 Enzyme Mechanisms
14 Enzyme Mechanisms

17 Enzyme Mechanisms
19 Enzyme Mechanisms
21 Regulation

24 Regulation
26 Regulation
28 Integration of Metabolism

May 1 Integration of Metabolism

3 Review
5 Review

11 Comprehensive Final Exam - 10:30-12:30

The instructor reserves the right to change by addition and/or subtraction any and/or
all materials contained in this syllabus. This includes, but is not limited to, course
content, assignments, due dates, and portion(s) of the grade assigned to individual
items within the course.

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 ADVANCED BIOCHEMISTRY
CHEM 5753, Spring 2006

Instructor Dr. Paul F. Cook

Phone 325-4581
Email pcook@chemdept.chem.ou.edu
Office PHSC 219A
Lectures MWF 8:30 - 10:20 AM, PHSC 201.
Office Hours MW 1:00 - 2:30 PM

Background
It is assumed that all students have a fundamental background in Biochemistry. Students
should try to be conversant with lecture topics prior to the lecture. A subjective portion
of the grade will be de rived from class participation. Additional reading assignments
from the text and the literature will be required.

Lectures will roughly follow the text, and students are required to have their own copy.
Lecture outlines, etc. will be pos ted on the Course Web site for CHEM 5753 at the
following URL address: http://cheminfo.ou.edu/~pfc//classes/index.html

OBJECTIVES

The course, CHEM 5753, Advanced Biochemistry, is designed to provide the student
with an overview of the principles underpinning the subject of biochemistry. A
prerequisite for this course is an underg raduate course in Biochemistry that covers
specifically metabolic pathways and a rudimentary knowledge of thermodynamics,
steady state kinetics, and enzyme regulation. Examination questions will be based on the
assumption that the student has a working knowledge of the above.

TEXTBOOK

Biochemistry 3rd Ed., Voet, D. & Voet, J. G., John Wiley & Sons, Inc., New York,
1995. ISBN 0-471-19350-x

Other texts that may also be helpful follow:

Biochemistry, 3rd Ed., Matthews, C. K., van Holde, K. E., & Ahern, K. G.
Addison, Wesley, Longman, Inc., San Francisco, 2000.
Biochemistry, 4th Ed., Zubay, G. Wm. C. Brown Publishers, Dubuque, 1996

GRADING

Grades will be calculated based on performance on the following:

Quizzes and Homeworks 300

Midterm exam 200
Final exam 300

Total = 800 pts.

Time allotted for quizzes will be 15 min. at the end of select class periods. Quizzes will
be unannounced. The dates of the hourly exams and the final exam are included in
the appended lecture schedule.

No makeup will be allowed for the 15 min. quizzes. Excused absences are only allowed
for the hourly exams, and makeup exams must be scheduled prior to the exam. (The
makeup exam may be either oral or written at t he discretion of the instructor.)
Homework assignments will not be accepted after the due date.

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The University of Oklahoma is committed to providing reasonable accommodation for
all students with disabilities. Students with disabilities who require accommodations
in this course are requested to speak with the insructor as early in the semester as
possible. Students with disabilities must be r egistered with the Office of Disability
Services prior to receiving accommodations in this course. The Office of D isability
Services is located in Goddard Health Center, Suite 166, phone 405/325-3852 or TDD
only 405/325-4173.

Each student should acquaint her or his self with the University's codes, policies, and
procedures involving academic misconduct, grievances, sexual and e thnic
harassment, and discrimination based on physical handicap.

LECTURE TOPICS AND SCHEDULE

Date Topic

Jan. 18 Introduction
20 How to Study Metabolism – Glycolysis & PPP

23 TCA & Gluconeogenesis

25 Fatty Acid Synthesis and β-Oxidation
27 Amino Acids

30 Nucleic Acids
Feb. 1 Thermodynamics - First Law
3 Thermodynamics - Second Law

6 Gibbs Free Energy

8 Chemical Energy - Generation and Storage
10 Redox Reactions

13 Redox Reactions
15 Introduction to Enzymes
17 Review

20 Exam 1

Feb. 22 Practical Considerations

24 Introduction to Kinetics

27 Enzyme Kinetics
Mar. 1 Enzymes - Nomenclature
3 Enzymes - Nomenclature

6 Bireactant Enzymes Reactions

8 Inhibition as a Mechanistic Tool
10 Product Inhibition

13 SPRING BREAK
15 SPRING BREAK
17 SPRING BREAK

20 Dead-End Inhibition
22 pH Dependence of Kinetic Parameters
24 pH Dependence of Kinetic Parameters

27 Origins of Catalysis
29 Review
31 Exam 2

5
 Apr. 3 Origins of Catalysis
5 Origins of Catalysis
7 Enzyme Mechanisms

10 Enzyme Mechanisms
12 Enzyme Mechanisms
14 Enzyme Mechanisms

17 Enzyme Mechanisms
19 Enzyme Mechanisms
21 Regulation

24 Regulation
26 Regulation
28 Integration of Metabolism

May 1 Integration of Metabolism

3 Review
5 Review

11 Comprehensive Final Exam - 10:30-12:30

The topics listed below are reading assignments over which you will be tested. The
instructor will hold an extra session every Wednesday evening at 7 pm to answer
question that you may have on the reading assignments. You will have exams the same
time as the undergraduates, but they will be different and will include material from the
reading assignments. You will also have take home problem sets to do in place of most
of the quizzes.

ADDITIONAL TOPICS AND READING ASSIGNMENTS

Introduction Chapter 1
Water as Solvent Chapter 2
Weak Acids and Bases Chapter 2
Amino Acids/Peptide bond Chapter 4, 7
Secondary Structure Chapter 8
Protein Folding Chapter 9
Quaternary Structure - X-ray/NMR Chapter 8
Protein Sequencing Chapter 7
Carbohydrate Structure Chapter 11
Glycoproteins Chapter 11
Lipid Structure and Membranes Chapter 12
Nucleic Acid Chemistry/ Structure Chapters 6, 7

This syllabus is a guide. The instructor reserves the right to change any items contained in
this syllabus. This includes, but is not limited to: course content, scheduled dates, and
calculation of final grade.