Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 431

MWF 1300-1350 SCIA 460

Syllabus - Fall 2008

Office: SA560a
Office Hours: TRF 1100-1150; W 1400-1550 other times by appointment
Phone: x 5719
Home: 822-1116

Course Information & Learning Outcome Goals

Catalog Description:

CHEM 431 - CHEM 432. Biochemistry (5-5). One-year lecture/lab sequence. Topics include biochemical energetics, introductory metabolism, and the nature and mechanism of action of enzymes. Prereq for CHEM 431: CHEM 110, any calculus course and either CHEM 322 or 328 with C- or higher. Prereq for CHEM 432: CHEM 431 with a grade of C- or higher. Weekly: 3 hrs lect, 6 hrs lab.

Learning Outcomes:

CHEM 431 addresses the following Department of Chemistry learner outcomes. Successful students will be able to demonstrate:

  • an understanding of the principles of biochemistry and what they reveal about the nature of physical and biological reality;
  • proficiency in the application of mathematics at the pre-requisite algebra level to solving chemical problems;
  • proficiency in abstract reasoning;
  • sound ability in written scientific communication;
  • an understanding of the use of biochemical and mathematical models;
  • an understanding of the relationship of experimental observation to chemical theory and knowledge;
  • proficiency in spatial perception;
  • the fundamental chemical knowledge and skills needed in chemistry as well as in other disciplines;
  • proficiency and skill in performing laboratory techniques and in making and interpreting laboratory observations; and
  • an understanding of the theory and operation of modern laboratory instruments used in biochemistry
CHEM 431 also addresses the following Humboldt State University learner outcomes at low intensity, in which the learner outcome is included implicitly or occasionally:
  • critical/creative thinking, information acquisition and application and
  • social justice, environmental responsibility,  and economic improvement.
Texts, Required Materials etc.:
  • Nelson & Cox. Lehninger Principles of Biochemistry,5th ed., Freeman (2008).
  • Paselk. Biochemistry Pathway Diagrams. HUB
  • Boyer, Modern Experimental Biochemistry, 3rd ed., Prentice-Hall (2000).
  • Approved Safety Goggles Approved eye protection is required to do any lab work! (ANSI Z87.1 impact compliant plus splash protection: available at HSU Bookstore - goggles purchased elsewhere must be approved by your lab instructor prior to use).
  • Scientific calculator with logarithmic and exponential function capabilities.  Programmable calculators are not allowed for quizzes or examinations! Your quiz/exam calculator should also be used for homework.
  • Fees:  There is a student-approved laboratory fee of $20.00.

General Information

For those who need a review of organic chemistry, I have in my office: Rodwell, Organic Chemistry (A brief review). This is a good, very brief, review of most of what you should know about organic chemistry reactions prior to taking biochemistry.

Lecture text: My attitude towards lecture texts is that they are references to repeat, expand, clarify (or confuse!), and otherwise aid you in your endeavor to understand biochemistry. I do not "require" that you buy a text - you're an adult, you should know what you require to "get through" a course. It's your decision. However, I strongly recommend purchasing a book. Nelson & Cox will be the central text for most of this course. Nelson & Cox and I may sometimes disagree (its my first time using this text, so I'm not certain, but its very likely we will have differences of opinion!). In such cases of disagreement between a text and myself, I am the "ultimate authority" and you must "do it my way." This doesn't mean that I am right, but rather that we need a common, defined set of knowledge for effective communication.

Lab text: Unlike lecture texts, laboratory texts and materials are often essential. You must have the laboratory text - most of your experimental work is described therein. The technique chapter readings are less essential. However, previous students have noted that such material is really valuable and it would have saved them some grief if they had started paying real attention to it early in the course. Note that additional lab materials are/will be posted on my Moodle site for Chem 431 Lab - you should check it at the beginning of each experiment!

The Biochemistry Pathway Diagrams are intended to aid you in taking notes - they will save you from having to rapidly copy many pathways, structures, etc. I recommend you bring them to lecture as we reach them and use them as part of your notes.

I have been posting a more or less complete set of my lecture notes in biochemistry every year since 1996. Both minor and major changes have occurred every year.

Over the years my notes have gotten better, but old errors still exist, and new errors will arrive with the expansions and updates for this course. If you use the notes and think you've found an error please tell me via e-mail. My lecture notes from last year's Chem 431 are also available to you with this caveat - there will be differences in what is covered and of fact. However if you wish to use them to "preview" what is likely to be covered next, please feel free.

I have traditionally tried to emphasize thinking and problem solving in this course and intend to continue. Thus there will be exam questions with answers you haven't seen and there will be synthesis questions. You can pass the course without "getting" these questions, but you won't get an "A."

Recommended Learning Strategies

  • DO NOT rely on my web notes - they have served many students in my other courses as an excellent way to check their notes, but make sure you do take your own notes! Most students find taking notes a very valuable learning experience.
  • Don't miss lecture or lab. You will be tested on lecture and lab material.
  • Go to class and take thorough notes. This will greatly improve your chances of getting a good grade.
  • Review the assigned material in the text and lab book before and after lecture and laboratory sessions. This can seem like a lot of extra work, but doing this will help you understand the material more than you may realize.
  • Don't procrastinate! Chemistry is not a subject that one can learn overnight."

Time Commitment:

Most students find chemistry to be a challenging and time consuming experience. An average student should expect to spend two hours out of class for each lecture hour in class and about one hour per lab hour, for a "C" grade, that is about 12 hours a week in study, preparation, lab write-ups, etc.


Lecture Calendar: See Fundamentals of Chemistry on my Web Page (

Laboratory Calendar: See Fundamentals of Chemistry on my Web Page (

Grading Information


Lecture: Attendance in lecture will not be taken.

Lab: Laboratory attendance is mandatory. All students are expected to attend labs during the normal hours at the beginning of the semester. Later in the semester I expect to allow students to have keys and to work in lab at other times between 0800 and 1700. However, you must still attend the initial introductory lab lectures at the beginning of each experiment. Make sure you are punctual at these meetings to get important safety and operational information!

Bring a scientific calculator to every laboratory. Come prepared to the labs - i.e., know what you are about to do in lab. It is expected that you will be prepared to participate in some discussion.

Exams: Note the in-class exam dates and be certain you can make them:

Exam I (Weeks 1-7) - Thursday, October 16

Exam II (Weeks 8-12) - Exam II - Thursday, November 20

Final Exam (Comprehensive): Monday 15 December 1240-1430

You will note the hour exams are being given during Thursday lab periods. This will allow you to have extra time to finish the exams (you will have two hours to complete a one-hour exam). The Final will have a normal time (two hours for a two hour exam).

Grading Points


 Midterm exams:

 2 @ 100 pts. each

  200 pts.

 Final exam:  

  200 pts.


Lab Final

100 pts.

100 pts.

Lab Notebook

150 pts.

150 pts.

Lab Write-ups

150 pts.

150 pts.


 Total =

800 pts.

Grading Rubric

  • Your grade is determined on your total points based on the percentage cut-offs listed below:
    A = 95%; A- = 90%; B+ = 87%; B = 84%; B- = 80%; C+ = 75%; C = 70%; C- = 65%; D+ = 58%; D = 50%.
  • The actual distribution will be adjusted at the end of the semester with 100% set to a number less than the total number of points based on class performance. In the past I have often used the percentage of total points achieved by the top student as 100%. For example, if the top student received 90% of total points, then an "A" would be 95% of 90% = 85.5%. However, I often adjust the 100% score based on my three decades of experience as our class size does not guarantee a reasonable statistical distribution.

Drop Policy:

I will give you until I return the first hour exam to drop this class with a "W." After that time, failure or other academic problems, as well as time management (work, kids, etc., but see below) will not be considered to be among the category of "serious and compelling reasons" needed to drop this course. Serious and compelling reasons are considered to be problems outside of the student's control and which could not be anticipated, such as serious illness or hospitalization. If you do have a problem, please notify me as soon as possible if you think it may require your dropping the class.


Incompletes are generally reserved for students who are unable to complete the class for serious and compelling reasons which occur after the last drop period.

Campus Resources for Students

Students with Disabilities

  • Disabilities may interfere with your success in this class. Students who wish to request disability-related accommodations should contact the Student Disability Resource Center in House 71, 826-4678 (voice) or 826-5392 (TDD).  Such accommodations may take up to several weeks to arrange. <>
  • Students needing accommodations should also contact the lecture instructor as soon as possible to facilitate/optimize their situation.
    • Note that all students will receive double-time for the two hour exams. However, if you qualify for extra time special accommodations will be needed for the Final.

Student Support organizations

  • The Indian Natural Resource, Science and Engineering Program (INRSEP) is a student support program designed for American Indian, Alaska Native, and Native Hawaiian students pursuing degrees in the natural resource and science disciplines under the College of Natural Resources and Sciences (CNRS) at Humboldt State University (HSU). <>

HSU Add/Drop Policy

Emergency Evacuation

Academic Honesty

Attendance and Disruptive Behavior



C431 Home

C431 Lecture Notes

© R A Paselk

Last modified 26 August 2008