Dr. Henry Jakubowski


TIME: 9:40 -10:50 AM, Days 2-4-6

ROOM: Ardolf 127

OFFICE: Ardolf 245; If I am not in my office, I can often be found in the computer lab, ASC 233

OFFICE HOURS: 11:00 -12:00 p.m., days 2-4-6, by appointment, or anytime you can find me

SYLLABUS: Since the syllabus is on line, I will add reading assignments from the text as the course progresses.


Since I have developed an Online Study Guide (OLSG) and many related web sites for this course which are available through the home page for the course.  Hence,  I am not requiring you to purchase an actual text. In the past I have used Biochemistry, 2nd. edition, by Garret and Grisham, but lately I have used the book in the class only as an additional reference. I do not follow the book sequentially, and supplement it liberally. In addition, this book contains much more material than we can cover in a one semester course.

I will place a copy of this book on reserve in Clemens Library for your use. I believe it is very useful to read a biochemistry text during the course to get an alternative presentation of the topics we cover. Likewise, if any of you are chemistry majors with a biochemistry concentration, and/or planning to attend graduate school in biochemistry or medical school, I would highly suggest that you purchase a biochemistry text, either through the bookstore or through the web (, Different books would be useful for different circumstances:

If you plan to attend graduate school in Biochemistry/Molecular Biology, or Biotechnology, I would suggest one of the following books:

  • Biochemistry by Garrett and Grisham. (Here is a great interactive site accompanying Garrett and Grisham's text:  Biochemistry )
  • Biochemistry by Voet and Voet
  • Biochemistry by Mathews and van Holde
  • Biochemistry by Rodney Boyer

If you plan to attend Medical School or are more "biologically oriented", I would suggest:

  • Biochemistry by Stryer
  • Principles of Biochemistry by Lehninger, Nelson, and Cox. (Here is a great interactive site accompanying Lehninger's book:  Principles of Biochemistry
  • Textbook of Biochemistry with Clinical Correlations by Devlin

Please read the following material on your own. It will not be covered directly in class, but you will be required to know the material.

BACKGROUND MATERIAL:  The reading material below is (from Garrett and Grisham.  If you purchase another text, search the table of contents and index to determine the appropriate reading material.

Chapt 1 - Chemistry is the Logic of Biological Phenomena

Chapt 32 - The Genetic Code; 1069-1074. [Given a DNA coding sequence, you must be able to determine the corresponding protein sequence.

The rest of the assignments are suggested readings. We will follow the material chronologically as listed.


Chapt 8 - Lipids

Chapt 9 - Membranes (to page 270).


Chapt 4 - Amino Acids

Chapt 5 - Proteins: Biological Function and Primary Structure (Appendix covered in lab)

Chapt 6 - Proteins: Secondary, Tertiary, and Quaternary Structure

Chapt 9 - Membranes: 9.2 - Structure of Membrane Proteins


Chapt 7 - Carbohydrates

Chapt 9 - Membranes: 9.3 - Membrane and Cell-Surface Polysaccharides; 9.4 - Glycoproteins


Chapt 11 - Nucleotides and Nucleic Acids

Chapt 12 - Structure of Nucleic Acids

Chapt 8 - Recombinant DNA


Chapt 15 - Enzyme Specificity and Allosteric Regulation, 460-462;

Chapt 15 Special Focus - Hemoglobin and Myoglobin, 480-493.

Chapt 15: Allosteric Enzymes, 469-480


Chapt 10 - Membrane Transport, 296-300.


Chapt 14 - Enzyme Kinetics

Chapt 15 - Enzyme Specificity and Allosteric Regulation


Chapt 16 - Mechanisms of Enzyme Action

Chapt 18 - Metabolism: An Overview; special emphasis on coenzymes and vitamins

Supplement - Enzyme catalyzed reactions in organic solvents


Supplement - The Chemistry of Dioxygen

Biological Oxidation Reactions - Dehydrogenases, Mono and Dioxygenases, and Oxidases;

Chapt 18 - Metabolism: An Overview

Chapt 3 - 3.6-3.7: High Energy Biomolecules, 66-79

ATP and Oxidative Phosphorylation Reactions in Glycolysis - pg 622-630;

Chapt 21 - Electron Transport and Oxidative Phosphorylation

Chapt 22 - Photosynthesis; pg 709-730


Chapter 10: (Membrane Transport) Energy Transduction - Uses of ATP - Active Transport 300-325

Supplement: Excitable Membranes, Neurotransmission, and Sensory Systems -Signal Transduction: Nerve Cells - Neural Chemistry; S41-63

Chapter 34: Signal Transduction at Cell Membranes - Protein Kinases/Phosphatases S1-S40

Tentative Class Schedule



  1. to understand the structure of proteins, nucleic acids, and lipids
  2. to understand how structure of biological macromolecules mediates function
  3. to understand the thermodynamics, kinetics, and intermolecular forces involved in the folding and stabilization of molecular aggregates and macromolecules
  4. to understand the thermodynamics, kinetics, and intermolecular forces involved in binding interactions (all biochemical events start with binding)
  5. to understand the thermodynamics, kinetics, and organic mechanisms involved in typical transport and enzyme-catalyzed reactions.


  1. to understand AND INTEGRATE the role of organic, physical, analytical and inorganic chemistry, AND biology and medicine in the science of biochemistry
  2. to realize the impact of the present biochemical revolution on the scientific, cultural, political, religious, economic institution of tomorrow.
  3. to develop critical thinking and analysis skills
  4. to integrate your ability to study (course) and do (lab) chemistry



Two exams (not counting the final) will be given during the semester. These exams will not be taken in class, but rather can be obtained from the secretaries in Ardolf. They must be completed without use of books, notes, or consultation with other people, (unless otherwise directed) and must be taken in an empty room in Ardolf. Return the exam to the secretaries when finished. I do not test rote memorization, although you must know the essential vocabulary of biochemical structures to do well. I will test your understanding of the concepts discussed, and most often will ask questions on material not directly covered in class. You should be able to answer the questions if you can apply the fundamental knowledge you acquire to other biological molecules. Examples of test questions would include analysis of data taken from recent publication. Makeups will only be allowed for certified emergencies. The makeup will be more difficult than the original, and consist of in depth essay questions or problems. The problems may be any combination of oral or written. Since they will be only two regular course exams, I will drop the lower of these exams and replace it with the final exam grade, if the final exam grade is higher than your lower test grade during the semester. In that scenario, you final exam grade will effectively count twice.

I will attempt to integrate class and lab as much as possible. To integrate the  lab understanding into the course in a formal way, I may include problems on the tests that derive from laboratory discussions and experiments, the investigatory experiments outlined in the On LIne Lab Manual, as well a series of summative questions found there. 




Several problem sets and other types of questions will be assigned and should be turned in on time. Only select question(s) will be graded on a random basis. It is important that you understand the problem assignments. The problem sets will often be questions derived from readings from recent published articles. In addition, we will have a series of in-class quizzes during the semester. These will last only 5-10 minutes. They might require the drawing of specific structures. One quiz chosen randomly from a given group might be graded and the resulting grade applied to all members of the group. In addition, group projects might be performed in class.



Each laboratory group will record a molecular modeling video describing the physical and chemical characteristics of an assigned protein. You will use the program Insight II on the Silicon Graphic network for the modeling and recording. Alternatively, you may use Chime, a program for modeling on the web.  Details to follow.


The exam will consists of a cumulative multiple choice exam given at the assigned final time, as shown above.


Participation in the course contributes 5% to your final grade.   Participation suggests interest and effort. It is not limited to just asking/answering questions in class.  It is not just doing the absolute minimum of work.  It includes asking questions outside of class when you don't understand the material. It includes submitting credible lab reports. It includes doing a thorough job on Lab 6 (investigatory lab) which means designing well controlled lab experiments and interpreting your data. I


This is a one semester course in biochemistry. Most biochemistry   books total around 1000 pages. You must conclude, as I and others have, that biochemistry can not be taught appropriately in a one semester course; all I can do is offer you an introduction. We will study aspects of biochemistry that run the gamut of what biochemists study today. Metabolism, just one facet of the field, will be de-emphasized, since it can not be taught in any kind of rigorous way in just part of a semester. Although students often do not like to skip around the book, that is exactly what we will do, in order to discuss the most contemporary areas of current research. I WILL NOT LECTURE DIRECTLY FROM ANY BOOK. The books describe above are well written, and will give you alternative explanations for the topics we will discuss. Use the book as reference if you choose to purchase one.


I will make extensive use of computer-assisted learning  in this class.  this will include

As an assignment for the second class, select the following link, which will help you become familiarized with the interactive web functionInteractive Web Functions


You will be using two different programs on the Silicon Graphics workstations in the computer lab. These include the programs Spartan and Insight II. You will use these programs for your final laboratory project as described in the laboratory syllabus, as well as for course work. I expect that you and I will often be frustrated as well collectively figure out how to use the programs. The alternative, not being frustrated by not using them, would be an incredible waste of an amazing learning opportunity. Please be patient as we develop expertise in use of both the hardware and software.


I reserve the right to make changes in the syllabus if class conditions suggest that these changes would provide a better learning environment for the class.