SYLLAUBS BCHM322 - Biochemistry I(I) - Spring 13



Dr. Henry Jakubowski



AN OVERVIEW OF BCHEM 322:  Two Courses for the Price of One

In the past, BCHM 322 has been offered in the Fall as the 1st course for Biochemistry majors and as an optional course for Chemistry majors, who comprised and still comprise the majority of the students.  This year, the course is offered in the second semester as the second course for biochemistry majors but still as the first biochemistry class for chemistry majors.   How will the class be structured to benefit both groups?

My overall focus will be the same:  to cover the major questions in biology from a chemical perspective.  I will follow the same over all topics as in previous years, since I strongly believe that chemistry major should be exposed to some of the biggest questions in biology.  Since the two groups have different backgrounds, I will significantly differentiate the labs and the expectations I have for the more biologically-based course content for the two groups. 

Chemistry majors: You may have a stronger background and interest in traditional chemistry.  This group will do all of the traditional labs, ending with a final investigative lab.  Certain content in the online book which is more biologically focused may be optional.

Biochemistry majors:  You will have a stronger background in biology and biochemistry.  This group will be expected to develop deeper understandings of areas requiring a greater biology background such as signal transduction, control of gene transcription to a greater depth.  In addition, they will be expected to have greater skills in reading biochemistry literature.   In forming class groups, I will ask biochemistry majors to lead the small group and class discussions, especially as we discuss literature findings.  In the lab, biochemistry majors will  do some  of the same labs as the chemistry major group, but when labs are similar to those done last fall in BCHM 1, they will do research-based project labs instead.     



Students will develop an understanding of

  1. the structure and function of proteins, nucleic acids, carbohydrates and lipids;
  2. the thermodynamics, kinetics, and intermolecular forces involved in the folding and stabilization of molecular aggregates and macromolecules;
  3. the thermodynamics, kinetics, and intermolecular forces involved in binding interactions;
  4. the thermodynamics, kinetics, and organic mechanisms involved in typical transport and enzyme-catalyzed reactions.


Students will develop

  1. their ability to synthesize and integrate content and ideas from organic, physical, analytical and inorganic chemistry, AND biology, in the study of complex biological molecules and systems and their regulation;
  2. critical thinking and analysis skills (i.e. problem solving skills);
  3. their ability to apply their understanding of course content to new problems derived from the biochemistry literature.


I have developed an online book for the course, Biochemistry Online:  A Course Based in Chemical Logic, and many related web sites for this course which are available through the home page for the course.  Hence,  I will not require students  to purchase an actual text, unless they are majoring in Biochemistry.  For Biochemistry majors, you will have already purchased the book used in Biochemistry I, Voet, Voet & Pratt Fundamentals of Biochemistry 2nd Edition.  For those of you who don't have a book, I will place a copy of  Biochemistry, 4th edition, by Garret and Grisham, on reserve in the library.  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.  If you choose to read an ancillary text, select the chapters relevant to the material covered.  For your convenience I've provided a supportive reading list of chapters from Garrett and Grisham that correspond to the sequence and content of BCHM 322.

In addition, many biochemistry texts have supplementary web sites.  Here are some useful links: 



  • Mini Exams 40% (3 X 13.333% each)
  • Quizzes (including Clickers), 5%
  • Submitted group work 5%
  • BCOnline preclass work 5%
  • Moodle: 5%
  • Sapling: 10%
  • Laboratory,15%
  • Final Exam, 15%

Grade Cutoffs:

The Cutoffs for grades will be no higher than shown below

Grade cutoffs

Class participation:  no fixed percentage.  If you actively participate in a significant way, I may change your grade 1/2 step (AB to A for example) if you are close to the cutoff for the higher grade.

Extra credit:  I may announce that some assignments are optional and could be used for extra credit.  I will assess the demands (time required, difficulty) of the optional assignments and assign your submitted assignment a point value based on the demands of the assignment and the quality of your submission.  If you are very close to a cutoff for a higher grade, the extra credit assignment may boost you to that grade.  Simply doing extra credit assignments, if available, won't boost your grade.


I find a blend of lecture and group activities to be most effective.  The more I teach, the less I rely on lecture.  Here are some really interesting ideas from Eric Mazur from Harvard on the role of lecture.

""The traditional approach to teaching reduces education to a transfer of information. Before the industrial revolution, when books were not yet mass commodities, the lecture method was the only way to transfer information from one generation to the next. However, education is so much more than just information transfer, especially in science. New information needs to be connected to preexisting knowledge in the student's mind. Students need to develop models to see how science works. Instead, my students were relying on rote memorization. Reflecting on my own education, I believe that I also often relied on rote memorization. Information transmitted in lectures stayed in my brain until I had to draw upon it for an exam. I once heard somebody describe the lecture method as a process whereby the lecture notes of the instructor get transferred to the notebooks of the students without passing through the brains of either. That is essentially what is happening in classrooms around the globe.'

"Since this agonizing discovery, I have begun to turn this traditional information-transfer model of education upside down. The responsibility for gathering information now rests squarely on the shoulders of the students. They must read material before coming to class, so that class time can be devoted to discussions, peer interactions, and time to assimilate and think. Instead of teaching by telling, I am teaching by questioning."  Science, 323, 50 (2009)

We'll start the class with student questions, a summary of the day's topics, and a review of student's submissions to preclass questions/assignments/online problems.  The rest of the class will be devoted to group work using the Workbook, student presentations, mini-lectures, or a combination, based on what seems best for the topic.  Quizzes will usually occur at the beginning of class.

In this student-centered approach, the responsibility is on you to have completed the assignments (reading, problems) before class.  In class I will address your specific questions (not questions like I don't understand any of the material), and we will do problems.


Some of you are biochemistry majors and are finally taking your first biochemistry class.  Others are chemistry majors who are chemistry majors, in part, because they didn't like biology earlier in their studies.  Some will be natural science or biology majors who opted for this course.  Each you brings in your own unique background and expectations to this course which requires understandings in chemistry and biology.   Each one of you comes in with your own motivations for taking this course (from it's a requirement to having a strong desire to learn biochemistry).   I also bring in my own expectations based on my own interests and background, and my experiences teaching this class.

You are all juniors and seniors.  By now you should have figured out what it takes to do well in an upper division science class and lab.   I view my job as a facilitator to help you learn the material.  I can't make you learn it.  I'll combine lecture, group work, labs, exams, and computer use to help you learn, but ultimately it's up to you to do what it takes to learn biochemistry.    I expect you to do the readings and assignments, ask question and seek help if you do not understand the material.  We will be studying some very difficult and new concepts and some easier ones you have encountered before.    We start from the simple (relatively speaking) - lipid - and move to the complex - how cells respond to signals. The course is cumulative, so you must keep up with the work.  Here is a list of important ideas that will help you do well in this course.

  1. Content is important

  2. At a higher level, content serves as a medium for process.

  3. If you're planning to take the MCAT, please review all the metabolic pathways yourself.

  4. A large amount of work is due near the end of the semester.

  5. If you can understand the chemical and physical properties of small molecules, you can understand the properties of big ones.

  6. The course builds an early foundation and grows from there, so please keep up with the work.

  7. You will reap what you sow. You will get out of this course what you choose to put into it.

  8. Decide why you are taking this course and what you wish to get out of it. Be honest with yourself.

  9. Hard work will payoff.

  10. The books are great references.

  11. Concentrate on process skill, not memorization.

  12. Little growth occurs without challenge.

  13. If you seek help you will find help.

  14. No one leaves my office understanding less than when they walked in.

  15. This course is a great way to review and learn Chemistry.

  16. A recommendation from a former A student

Here is what I expect from students:

  • You will treat everyone in the class, including the professor, with the respect.
  • You will attend every class, give your full attention to the material, and conduct yourself in an appropriate manner.
  • You will agree to do the work outlined in the syllabus on time.
  • You will acknowledge that previous academic preparation (e.g., writing skills) will affect your performance in this course.
  • You will acknowledge that your perception of effort, by itself, is not enough to justify a distinguished grade.
  • You will not plagiarize or otherwise steal the work of others.
  • You will not make excuses for your failure to do what you ought.
  • You will accept the consequences -- good and bad -- of your actions.

Here is what you can expect from me:

  • I will treat you with the respect.
  • I will not discriminate against you on the basis of your identity or your well-informed viewpoints.
  • I will manage the class in a professional manner. That may include educating you in appropriate behavior.
  • I will prepare carefully for every class.
  • I will begin and end class on time.
  • I will teach only in areas of my professional expertise. If I do not know something, I will say so.
  • I will return your assignments as quickly as possible.
  • I will pursue the maximum punishment for plagiarism, cheating, and other violations of academic integrity.
  • I will keep careful records of your attendance, performance, and progress.
  • I will make myself available to you for advising.
  • I will maintain confidentiality concerning your performance.
  • I will provide you with professional support and write recommendations for you if appropriate.
  • I will be honest with you.
  • Your grade will reflect the quality of your work and nothing else.
  • I am interested in your feedback about the class, but I am more interested in what you learned than how you feel.


Three mini 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.  I will drop the lowest 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, your 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. 


  • Mini Test 1:  Lipids and Proteins T 2/19-R 2/21
  • Mini Test 2:  CHO and Binding Wed 3/13-Fri 3/15
  • Mini Test 3:  Diffusion, Enzyme Kinetics, Enzyme Mechanisms: Wed 4/17-Fri 4/19
  • Final Exam:  Thursday, May 9, 10:30 AM -12:30 PM - Computer Room - ASC 135, CSB


These questions are meant to help (if not force) you to learn the material.  Completion of these will count toward the 25% of your final grade that derives from Quizzes, Problem Sets, Online preclass and homework questions), Group Work.  I won't grade these based on % correct exclusively but on both % correct and completion of the assignments.


I will use Moodle for online multiple choice problems (called quizzes in Moodle).  In addition I will post answer keys, some Power Points, and interesting literature that relates to topics we discuss in class.  I have placed a link to Moodle on each day of the class schedule that you should completed a Moodle Quiz as an assignment for that class.  I expect you to complete these before 8:30 AM of the class day.  A few of the quiz questions are more designed for Biochemistry majors that have already taken a biochemistry class.  These questions start with BCHM.    If you have not used Moodle, here are some instructions:

  • Go to Moodle or find it through the search indices on the CSB/SJU Homepage

  • Enter you CSB/SJU network username and password and click "Login"

  • Click the link to BCHM 322 under the "My Courses" column.

Sapling Online Problems

Sapling Online Problems is similar to other online homework you have had in previous courses (Connect, OWL, etc).  The Sapling problems are more complex than simple multiple choice and require drawing of chemical structure, making calculations, moving structures to match with properties, etc.  IN CONTRAST TO Moodle problems, the Sapling Online Problems are due at the end of each Chapter (1-9).   I have placed a link to the Sapling problems on last day we spend on a given chapter.  That is the due date for the problems.  As with Moodle, your grade for these will count towards the 25% of the course grade derived from Quizzes, Problem Sets, Online preclass and homework questions), Group Work.  Here are instructions for it's use.  It costs $29.99/student.  You may be prompted for a enrollment key.  Use 1797 or whatever the last 4 digits of number are on the address.

  1. Go to

  2. If you already have a Sapling Learning account, log in, then skip to step 5. 

  3.  If you have a Facebook account, you can use it to quickly create a Sapling Learning account. Click the blue button with the Facebook symbol on it (just to the left of the username field). The form will auto-fill with information from your Facebook account (you may need to log into Facebook in the popup window first). Choose a password and time zone, accept the site policy agreement, and click "Create my new account". You can then skip to step 5. 

  4. Otherwise, click "Register here" or �Create an Account.� Supply the requested information and click "Create my new account". Check your email (and spam filter) for a message from Sapling Learning and click on the link provided in that email.

  5. Find your course in the expandable list (sorted by subject, term, and instructor) and click the title link. 

  6. Select a payment option and follow the remaining instructions.   Once you have registered and enrolled, you can log in at any time to complete or review your homework assignments.

  7. During sign up - and throughout the term - if you have any technical problems or grading issues, send an email to explaining the issue. The Sapling support team is almost always more able (and more quick) to resolve issues than your instructor.        

X out of the browser if you wish to complete the Sapling assignment at a future date. Do not select the Exit icon within the Sapling assignment.

BC Online Pre-Class Questions:

These are imbedded into BC Online and must be submitted by 8:30 of the morning of class. When you submit your answers, I receive a time stamp as well. I use your responses to tailor the ensuing class.  These question usually require a written response.


We will do a lot of group work in class using the Workbook that you will purchase from the bookstore.  You will also submit answers to questions Several problem sets and other types of questions will be assigned and should be turned in on time. Only selected 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.


  • Approximately 10 labs; Attendance is mandatory. Part of each lab will be devoted to a summary on the topic of the lab.
  • For grading of the laboratory component of the course, and for a detail laboratory syllabus, see the laboratory manual
  • The overall lab grade will count 20% of the final grade for the course.


We will use a variety of modeling programs including  SPARTAN, VMD, and Deep View (SPDV) ) for modeling.   Please be patient as you develop expertise in use of these programs. You will use these for labs, problem sets, and extra credit..


The exam will consists of a cumulative multiple choice exam given at the assigned final time, as shown above.  For practices multiple-choice questions, go to the interactive site accompanying Garrett and Grisham's text, Biochemistry, 2nd ed., and select student links which leads to quiz questions.


Participation in the course may move you up a half grade step if you are on the border of the higher 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

  • email -   I will ask you to check for messages daily. these messages might include assignments for the next class, announcement of quizzes, etc; 
  • interactive web questions - These will be imbedded in the online text and will include pre-class question, online multiple choice quizzes, and discussion forum questions;
  • online quizzes using Moodle;
  • online homework through Sapling Learning


One of the process goals of this course is to increase your ability to apply your understanding of course content to new problems derived from the biochemistry literature.  I have created a series of literature-based learning modules that will provide you an opportunity to analyze biochemical data and draw appropriate conclusions in a way which is highly defined and contextual, while exposing you in an incremental manner to modern literature.  They will also serve to prepare you for class examinations. 


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.