Advanced Biochemistry CHEM 4753
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1 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 [email protected] Office PHSC 219A Lectures MWF 8:30 – 9:20 AM, PHSC 201. Office Hours MW 1:00 PM - 2:30 PM 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. Background 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 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 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.
Transcript of Advanced Biochemistry CHEM 4753
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Advanced BiochemistryCHEM 4753
Dr. Paul F. CookDepartment of Chemistry and Biochemistry
University of Oklahoma
ADVANCED BIOCHEMISTRYCHEM 4753, Spring 2006
Instructor Dr. Paul F. CookPhone 325-4581Email [email protected] PHSC 219ALectures MWF 8:30 – 9:20 AM, PHSC 201.Office Hours MW 1:00 PM - 2:30 PM
It is assumed that all students have a fundamental background in Biochemistry. Studentsshould try to be conversant with lecture topics prior to the lecture. A subjective portionof the grade will be de rived from class participation. Additional reading assignmentsfrom the text and the literature will be required.
Background
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 thefollowing URL address: http://cheminfo.ou.edu/~pfc//classes/index.html
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
OBJECTIVES
This course will provide a con tinuation of the material presented in CHEM 3653Introduction to Biochemistry. As a result, the introductory course is a prerequisite. Thecourse will build on the student's general background in biochemistry, and will considertopics 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 bestressed overall.
The class will move at a rapid pace because of the amount of material to be covered, andthus one should try to stay slightly ahead of the lecture schedule with respect to readingassignments. Staying ahead will also allow the student to derive most from the lectures.
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ESTIMATION OF GRADE
Grades will be calculated based on t he student’s performance on a number ofexaminations, 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 andtheir value is provided below:
Quizzes and Homework 300Hourly Exams 300Final* 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 NOMAKE-UPS FOR QUIZZES!
Hourly exam dates and the date of the final exam are provided below. Exams willinclude material covered in lecture and from reading assignments. MAKE-UP EXAMSWILL BE GIVEN ONLY IF THE INSTRUCTOR HAS BEEN NOTIFIED PRIORTO THE EXAM AND A PHYSICIAN’S NOTE, ETC. IS PROVIDED!
*The standardized American Chemical Society exam in Biochemistry will be used asthe 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 takeclass 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, andprocedures involving academic misconduct, grievances, sexual and ethnic harassment,and discrimination based on physical handicap.
REASONABLE ACCOMMODATION POLICY
Any student in this course who has a disability that may prevent her or h im from fullydemonstrating his or her abilities should contact me personally as soon as possible so wecan discuss accommodations necessary to ensure full participation and facilitate youreducational opportunities.
LECTURE TOPICS AND SCHEDULE
Date Topic
Jan. 18 Introduction20 How to Study Metabolism – Glycolysis & PPP
23 TCA & Gluconeogenesis25 Fatty Acid Synthesis and β-Oxidation27 Amino Acids
30 Nucleic AcidsFeb. 1 Thermodynamics - First Law
3 Thermodynamics - Second Law
6 Gibbs Free Energy 8 Chemical Energy - Generation and Storage10 Redox Reactions
13 Redox Reactions15 Introduction to Enzymes17 Review
20 Exam 1
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Feb. 22 Practical Considerations24 Introduction to Kinetics
27 Enzyme KineticsMar. 1 Enzymes - Nomenclature
3 Enzymes - Nomenclature
6 Bireactant Enzymes Reactions 8 Inhibition as a Mechanistic Tool10 Product Inhibition
13 SPRING BREAK15 SPRING BREAK17 SPRING BREAK
20 Dead-End Inhibition22 pH Dependence of Kinetic Parameters24 pH Dependence of Kinetic Parameters
27 Origins of Catalysis29 Review31 Exam 2
Apr. 3 Origins of Catalysis 5 Origins of Catalysis 7 Enzyme Mechanisms
10 Enzyme Mechanisms12 Enzyme Mechanisms14 Enzyme Mechanisms
17 Enzyme Mechanisms19 Enzyme Mechanisms21 Regulation
24 Regulation26 Regulation28 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/orall materials contained in this syllabus. This includes, but is not limited to, coursecontent, assignments, due dates, and portion(s) of the grade assigned to individualitems within the course.
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ADVANCED BIOCHEMISTRYCHEM 5753, Spring 2006
Instructor Dr. Paul F. CookPhone 325-4581Email [email protected] PHSC 219ALectures MWF 8:30 - 10:20 AM, PHSC 201.Office Hours MW 1:00 - 2:30 PM
BackgroundIt is assumed that all students have a fundamental background in Biochemistry. Studentsshould try to be conversant with lecture topics prior to the lecture. A subjective portionof the grade will be de rived from class participation. Additional reading assignmentsfrom 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 thefollowing URL address: http://cheminfo.ou.edu/~pfc//classes/index.html
OBJECTIVES
The course, CHEM 5753, Advanced Biochemistry, is designed to provide the studentwith an overview of the principles underpinning the subject of biochemistry. Aprerequisite for this course is an underg raduate course in Biochemistry that coversspecifically metabolic pathways and a rudimentary knowledge of thermodynamics,steady state kinetics, and enzyme regulation. Examination questions will be based on theassumption 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 300Midterm exam 200Final exam 300
Total = 800 pts.
Time allotted for quizzes will be 15 min. at the end of select class periods. Quizzes willbe unannounced. The dates of the hourly exams and the final exam are included inthe appended lecture schedule.
No makeup will be allowed for the 15 min. quizzes. Excused absences are only allowedfor the hourly exams, and makeup exams must be scheduled prior to the exam. (Themakeup 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 forall students with disabilities. Students with disabilities who require accommodationsin this course are requested to speak with the insructor as early in the semester aspossible. Students with disabilities must be r egistered with the Office of DisabilityServices prior to receiving accommodations in this course. The Office of D isabilityServices is located in Goddard Health Center, Suite 166, phone 405/325-3852 or TDDonly 405/325-4173.
Each student should acquaint her or his self with the University's codes, policies, andprocedures involving academic misconduct, grievances, sexual and e thnicharassment, and discrimination based on physical handicap.
LECTURE TOPICS AND SCHEDULE
Date Topic
Jan. 18 Introduction20 How to Study Metabolism – Glycolysis & PPP
23 TCA & Gluconeogenesis25 Fatty Acid Synthesis and β-Oxidation27 Amino Acids
30 Nucleic AcidsFeb. 1 Thermodynamics - First Law
3 Thermodynamics - Second Law
6 Gibbs Free Energy 8 Chemical Energy - Generation and Storage10 Redox Reactions
13 Redox Reactions15 Introduction to Enzymes17 Review
20 Exam 1
Feb. 22 Practical Considerations24 Introduction to Kinetics
27 Enzyme KineticsMar. 1 Enzymes - Nomenclature
3 Enzymes - Nomenclature
6 Bireactant Enzymes Reactions 8 Inhibition as a Mechanistic Tool10 Product Inhibition
13 SPRING BREAK15 SPRING BREAK17 SPRING BREAK
20 Dead-End Inhibition22 pH Dependence of Kinetic Parameters24 pH Dependence of Kinetic Parameters
27 Origins of Catalysis29 Review31 Exam 2
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Apr. 3 Origins of Catalysis 5 Origins of Catalysis 7 Enzyme Mechanisms
10 Enzyme Mechanisms12 Enzyme Mechanisms14 Enzyme Mechanisms
17 Enzyme Mechanisms19 Enzyme Mechanisms21 Regulation
24 Regulation26 Regulation28 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. Theinstructor will hold an extra session every Wednesday evening at 7 pm to answerquestion that you may have on the reading assignments. You will have exams the sametime as the undergraduates, but they will be different and will include material from thereading assignments. You will also have take home problem sets to do in place of mostof the quizzes.
ADDITIONAL TOPICS AND READING ASSIGNMENTS
Introduction Chapter 1Water as Solvent Chapter 2Weak Acids and Bases Chapter 2Amino Acids/Peptide bond Chapter 4, 7Secondary Structure Chapter 8Protein Folding Chapter 9Quaternary Structure - X-ray/NMR Chapter 8Protein Sequencing Chapter 7Carbohydrate Structure Chapter 11Glycoproteins Chapter 11Lipid Structure and Membranes Chapter 12Nucleic Acid Chemistry/ Structure Chapters 6, 7
This syllabus is a guide. The instructor reserves the right to change any items contained inthis syllabus. This includes, but is not limited to: course content, scheduled dates, andcalculation of final grade.
