CHEM 451
Introductory Biochemistry
Fall 2004
Lecture M,W,F 9-9:50 AM, Rm. 304 Crawford Hall
Lab Tue. (section A) or Wed. (section B) 2-5 PM, Rm. 308 Crawford Hall
Dr. M. Werner
office: CRW 314, phone: 635-2281
email: mwerner@lssu.edu
Office hours: (In CRW 314) MWF, 10-11AM and M 2-4 PM, or by appointment. If I am not in my office I am
probably in the lab.
State Council of State Science Supervisors:
http://www.csss-science.org/safety.shtml
http://www.csss-science.org/downloads/scisafe.pdf
Required Text: Biochemistry by Mathews, VanHolde, and Ahern, 3rd ed. 2000
*Lecture Date
Mon. Aug. 30
Topics
Review of organic chem., , pH, pKa, and buffers
Unit #
1
Wed. Sept. 1
Central Dogma of Biochemistry, Amino Acids
1
Fri. Sept. 3
Interactive session
1
Mon. Sept. 6
No Class, Labor Day
No Class
Wed. Sept. 8
Cellular environment, water and non-covalent
interactions
Cellular environment, water and non-covalent
interactions
Interactive Session
Fri. Sept. 10
Mon. Sept. 13
Wed. Sept. 15
Introduction to energetics and ATP
Fri. Sept. 17
Base pairing, Central Dogma, enzymatic
coupling
Interactive Session
Mon. Sept. 20
Wed. Sept. 22
Fri. Sept. 24
*
Levels of Structure in Protein Architecture
Mon. Sept. 27
Protein Purification and Sequencing
Wed. Sept. 29
Interactive Session
Fri. Oct. 1
Enzyme Kinetics, Enzyme Inhibition
Mon. Oct. 4
Enzyme Mechanisms, Control of Enzymatic
Activity,
Membranes and Membrane Proteins
Wed. Oct. 6
Fri. Oct. 8
Interactive Session
Mon. Oct. 11
Wed. Oct. 13
Fri. Oct. 15
Mon. Oct. 18
Review Units 1-3 - UNIT 3
BENCHMARK
*
Mid-Term Exam – UNIT 6
2
2
2
3
3
3
3 BENCHMARK
4
4
4
5
5-6
6
5 and 6
1-6
BENCHMARK
No Class
Design of Metabolism,
7
Glycolysis
Wed. Oct. 20
Interactive Session
Fri. Oct. 22
The Pyruvate Dehydrogenase Complex and the
TCA Cycle
The Pentose Phosphate Pathway
Mon. Oct. 25
Wed. Oct. 27
Interactive Session
Fri. Oct. 29
Respiratory Chain, Proton Transport
Mon. Nov. 1
ATP Synthesis
Wed. Nov. 3
Interactive Session
Fri. Nov. 5
Light Reactions of Photosynthesis
Mon. Nov. 8
More Photosynthesis
Wed. Nov. 10
Fri. Nov. 12
*
Gluconeogenesis, CO2 Fixation
Mon. Nov. 15
Glycogen Degradation and Synthesis
Wed. Nov. 17
Dark Reactions of Photosynthesis
Fri. Nov. 29
Interactive Session
Mon. Nov. 22
7
8
8
8
9
9
9
9
9
UNIT 9
BENCHMARK
10
10
10
10
NO CLASS-THANKSGIVING
Wed. Nov. 24
NO CLASS-THANKSGIVING
Fri. Nov. 26
Fatty Acid Degradation
Mon. Nov. 29
Fatty Acid Synthesis
Wed. Dec. 1
Interactive Session
Fri. Dec. 3
Mon. Dec. 6
Interactive Session – UNIT 9 BENCHMARk
7
*
Frontiers in Biochemistry – UNIT 11
BENCHMARK
11
11
11
Don’t Miss this
class!! UNIT 11
BENCHMARK
Wed. Dec. 8
Review
Units 1-6
Fri. Dec 10
Review
Units 7-11
Wed. Dec. 15 (Rm304) Final Examination
*
7:30-9:30
AM
Indicates Unit Bench Mark. Failure to meet this benchmark will result in the loss of 50 Pts.
This is a tentative schedule and may be modified as I deem necessary.
Objective: My aim is to introduce you to the concepts necessary for understanding how the biological world works
at its most basic level, the chemical level. I realize that most of you have varied career plans, but if I can excite just
one of you enough to want to take another chemistry course or become involved in biochemical research or
applications, I have succeeded in my objective.
Format: This course is completely different than any other course that you have ever taken. THIS IS AN
INTERACTIVE COURSE. IT WILL REQUIRE YOU TO SPEAK, THINK, AND LEARN. What does that mean?
It means that you will only have two traditional lecture a week (Yeah, Baby!!!). It means that you will attend an
interactive session during regularly scheduled lecture time (usually Fridays). It means that you will be expected to
take your own notes (Some of you might be thinking, Sacrilege!). It means that you will be expected to know
material outlined in Unit Objectives available on the web. It means that you have to be disciplined (A major
accomplishment for some I know).
I have no doubt that those students that are motivated and disciplined will enjoy this course. Part of
learning science is the ability to take in information, highlight the key aspects, and incorporate it into your own
learning framework. How do you reach this “zen-like” utopia that we call scholarship? For a start, students need to
be able to discuss topics using the vocabulary of the discipline with their peers and teachers. In addition, students
need to be able to build their knowledge base by drawing on what they already know. I have found the traditional 3
lecture a week format ineffective at teaching these valuable tools. This course will allow you to learn biochemistry if
you are motivated and disciplined.
The course is divided into eleven units. Each unit consists of a reading assignment and a list of objectives. You will
find these objectives and online quizzes at the following website for the LSSU WebCT server:
http://webcta.lssu.edu
Once you log on to this website, you will be asked for a username and password. I will give these to you during the
first lecture. You will then be asked to add the course you are interested in. You should have access to add
Biochemistry I (under the Chemistry Section on WebCT). Follow the directions. Once logged on to the site you
should change your password. If you email me using WebCT by Friday Sept. 3th , I will give you an extra 10
pts.
The WebCT home page for Biochemistry I will have links for the course units, student webpages, and course
syllabus. If you click on the Course units icon, a new page containing each of the 11 units will display. To enter a
unit, click its folder. Each unit folder will contain a self-test, unit objectives, study tools, and a quiz folder. First,
click on the unit objectives and PRINT THEM OUT. You could do everything while still on the computer screen
but I highly discourage this practice. Use the study tools (often online links to helpful sites).
Once you have mastered all of the objectives, take the self-test. I recommend that you print this out and take the test
away from the computer. This is not graded and intended only to give you some assurance that you understand the
majority of the material. Then take the unit quiz online. These quizzes are worth 10 pts each, and you must pass
them all to pass the class. You will receive an F in the course if you do not pass all of the quizzes. You will
notice that there are 3 different forms of the unit quizzes. You must take the first form on your initial attempt. If
you pass then great, you can move on to the next unit. If you fail, you must wait 12 hr (one day) to take the next
quiz form number. Please take quizzes in their sequential order. If you do not pass the quiz for a unit on the
third attempt, you must come and see me during scheduled office hours to take an oral quiz.
There are four benchmarks throughout the semester as indicated in the schedule. You must complete the online
quizzes by these dates up to and including the indicated unit or YOU WILL LOOSE 50 PTS per benchmark
missed. These benchmarks are intended to discourage procrastination. An electronic record will be kept of your
performance on these online quizzes that I will track throughout the semester.
You should become familiar with all the material in the reading assignment. The quizzes and exams will, however,
focus on material detailed in the objectives. I recommend that you approach each unit in the following manner:
1. The weekend before we start a new unit, print the unit objectives and look them over to get an idea of what
material is considered most important. These documents will be in Adobe Acrobat (PDF) format. If you have
problems accessing these documents, see me immediately.
2. Read the sections of Mathews listed at the beginning of each unit (or subunit)
3. Go through the objectives in detail, looking up the answer to each one. I recommend that you write these
answers in the printed objectives or some other notebook. DO THIS BEFORE YOUR INTERACTIVE
SESSION. You may want to make a three ring binder to allow your written notes to be easily inserted. You
will find these notes tremendously useful as you review for quizzes and exams. It is an excellent idea to write
down page references in your notes. This practice will save you a lot of time when you want to refer to
something again.
4. Attend the interactive session. THESE SESSIONS ARE NOT INTENDED TO FILL IN THE BLANKS IN
YOUR OBJECTIVES. These sessions will consist of a brief discussion, followed by group directed problems.
You will be asked to present answers on the board and defend them. You will be expected to participate freely
and willingly. Your participation in the session will be graded and is worth 10 pts. for each session.
5. After you have had your interactive session, take the online unit quiz. Every unit will have an online quiz
that must be passed. IN ORDER TO PASS THE CLASS, YOU MUST PASS ALL THE ONLINE QUIZZES.
You are required to pass four benchmarks indicated in the schedule If you don’t you will lose 50 pts per
benchmrk.
Lectures: There will be two traditional lectures a week every Monday and Wednesday morning at 9 AM. I will
cover the major topics of the individual units at an approximate pace of 1 unit per week. I suggest you keep to this
pace for your mastery of unit material as well. Do not bring your text to lecture. Why? Focus your attention on the
lecture notes and the discussion going on in class. Don’t bother trying to flip through the text to see how my
presentation differs. I will extensively utilize assorted visual aids during the lectures as learning aids, most not from
the book. I will TRY to post any power point presentations on WebCT as well. BE PREPARED TO TAKE YOUR
OWN NOTES! I suggest a loose-leaf notebook for taking your notes. You will then attend the interactive sessions
either on Fri. during our regularly scheduled lecture hour.
Assigned Problems: The objectives give lots of sample problems, DO THEM. As we proceed into the semester, I
will be posting problems for our interactive sessions on WebCT. You will want to print these out before your
session and bring them with you. These problems are not graded, but your participation in their solution is. I
WILL NOT BE POSTING ANSWERS TO THESE QUESTIONS, SO SHOW UP!
Electronic study guide for Biochemistry (CD): In addition to doing all of the objectives, I strongly recommend
the use of the accompanying CD to study. I think you will find it very helpful, informative, and a good resource for
future use.
Attendance/Absences: This course will cover material quickly; it is very important that you attend the weekly
lectures and interactive sessions. No formal record of lecture attendance is maintained, however, I will be grading
your participation in the interactive sessions, so in essence I am taking role. If you have to miss an interactive
session, don’t worry too much about it, it is only worth 10 pts (11 sessions = 110 total pts). However, do come to
my office hours so that we can discuss what you missed. It is your responsibility to get any missed material from
another student. Attendance for exams is expected.
Exams: There will be one mid-term examination (Wed. Oct. 13th in our normal lecture room at 9am). This exam
will count for 20% of your grade. There are no makeups for any reason. If you have a problem with either the
mid-term or final exam, see me by Friday September 3th. A final exam will be administered on Wed. Dec. 15th at
7:30 AM-9:30AM (ooh that’s early, sorry!) in Crawford 304. This exam will have no makeups and will be worth
22% of your grade.
Quizzes: Every unit will have an online quiz that must be passed. IF YOU DO NOT PASS ALL THE
QUIZZES, YOU WILL RECEIVE AN F AT THE END OF THE SEMESTER. If you fail your first attempt of
the online quiz, you will not be allowed to take another quiz on the same unit until the next day (12 hr later). This
is meant to ensure that you study more and seek help if needed.
Extra Credit: 10 pts. if you email me on WebCT by Friday Sept. 3 rd. No other extra credit will be given except
in the form of a question on exams.
Lab: The purpose of the laboratory in CHEM 451 is to expose you to some of the basic techniques involved in
biochemical research. As seen in the grading scheme below, a major emphasis will be placed on your laboratory
participation. Biochemistry is a “hands on science”, and the labs are designed to expand what is presented in the
lecture. See lab syllabus for more details.
Grading:
Laboratory
Passing all Unit Quizzes
Interactive Sessions
Mid-term Exam
Final Exam
Total
360 points
110 points
110 points
200 points
220 points
1000 points
Point range
900-920 / 921-979 / 980-1000
800-820 / 821-879 / 880-899
700-720 / 721-779 / 780-799
570-599 / 600-659 / 660-699
0 - 569
Course grade
A- / A / A+
B- / B / B+
C- / C / C+
D- / D / D+
F
*I reserve the right to curve the grading scale as I deem necessary.
Regrade Policy: Laboratory reports will never be regraded. See me before turning them in if you have questions.
Online quizzes are either pass-fail. You will be expected to get 70% correct on these quizzes.
*I retain the right to change this syllabus, as I deem necessary at any time during the semester.
CHEM 451
Introductory Biochemistry Lab
Fall 2004
Lab Tue. (section A) or Wed. (section B) 2-5 PM, Rm. 308 Crawford Hall
Dr. M. Werner
office: CRW 314, phone: 635-2281
email: mwerner@lssu.edu
Required Lab text: Experiments in Biochemistry, A Hands on Approach, by Farrell and Ranallo
Required Lab
Extras: Lab Notebook with gridded carbon copy pages (available in the book store), Safety goggles or glasses
The purpose of the laboratory in CHEM 451 is to acquaint you with laboratory techniques encountered in
biochemical research and to give you practical experience in performing biochemical experiments. The experiments
were selected based on the techniques used, the biochemical molecules assayed and to some extent application to
lecture material.
You will need to purchase a lab notebook with gridded duplicate pages. Goggles or safety glasses are required
and your must have them prior to the beginning of the lab. Both notebooks and safety goggles are available at
the book store. Other materials needed: your brain and several permanent marking pens (Sharpies are the best)
Week of:
Aug. 29
Sept. 6
Sept 13
Sept 20
Sept. 27
Oct 4
Oct 11
Oct 18
Oct 25
Nov 1
Nov 8
Nov. 15
Nov 22
Nov. 29
Dec 6
Experiment Name
(Pts)
Check in: Pipeting and Buffers (30 for both)
NO LAB-Labor Day
Spectraphotometry, Beer’s Law
(30)
Enzyme purification, LDH
(30)
Ion exchange chromatography
(30)
Gel filtration chromatography
(30)
NO LAB
Protein Electrophoresis
(30)
Enzyme Kinetics, and [LDH]
(30)
Intro. to HPLC analysis
(30)
HPLC enzyme kinetics
(30)
LDH Research Presentations
(60)
NO LAB- Thanksgiving
Kinetics of Tyrosinase
(30)
Inhibition of Tyrosinase
(30)
Experiment in Lab Manual
Exp. 1 and Exp. 2
NO LAB
Exp. 3
Exp. 4a
Exp. 5a
Exp. 7a
NO LAB
Exp. 9c
Exp. 8a and 3a
Handout
Handout
na
NO LAB
Exp. 8
Exp. 8 and handout
Note: Labs are scheduled from 2-5, however, some labs may run over if you are not efficient in lab. Labs
from Sept. 20-Oct. 25 are the longer labs of the semester, so be prepared.
In order to complete the labs in the allotted time, you must be familiar with the lab procedure before the start of the
lab period. Read the complete experiment and do the prelab questions before coming to lab. Prelab questions will
be turned in at the beginning of each lab and graded as part of you lab grade. Keep in mind, in this biochemistry lab,
the results of one week will be used during subsequent weeks. Therefore, it is important that you understand what
you are doing at each step and why you are doing it. An error in step 5 of a 6 step procedure means that the previous
4 steps, no matter how well they were done, are for naught. If you are in doubt about what to do, ask, and remember
that old lab axiom, “Never throw anything away.”
Lab attendance/absences: Attendance is mandatory, and remember, “Don’t be on time, be early!” For grading
purposes, the best 10 lab grades will be counted out of 11. You MUST attend the LDH Research Presentations
and I will not allow you to drop this lab. Missed labs cannot be made up and will be recorded as a zero. Tardiness
will result in loss of points (every 5 min late equals 2 pts) and you may miss important last minute instructions for
the experiment. You will work with a partner for most experiments, make sure it is a team effort. If you do miss a
lab, make sure that you talk to your partner as well as me to find out what you need to do for the next lab.
Lab Notebook: It is imperative that you maintain a complete notebook. This notebook is to be separate from the
lab manual. Anyone should be able to take your notebook and understand what was done, what results were
obtained, and repeat the experiment. Write in the lab notebook with ballpoint pen, crossing through errors. Do not
remove original pages from the notebook. Your note book will be worth 5 pts. for each lab report (worth a total of
50 pts.) Lab notebook pages will be due the following week along with your analysis sheets from the lab manual.
The lab notebook is to contain:
1.
Your name, course name, and section number on the cover.
2.
A table of contents on the first few pages
3.
All your data, calculations, last minute modifications to the protocols, graphs, results, and conclusions must
be in the notebook. Do not use scraps of paper to record any of these items.
4.
Each page needs to show your name (and your partner's name), date, and experiment title.
5.
Results should describe the results obtained (i.e. raw data and all calculations used to obtain "processed"
data, tables and rough graphs). Final graphs, to be turned in, should be done on either a computer or with
10 mm x 10 mm graph paper.
6.
Discussion should analyze and interpret results obtained.
Safety:
1. Safety goggles or glasses must be worn at all times!!
2. Appropriate dress is required.
3. Report all injuries to me.
4. No smoking, eating, or drinking in the laboratory.
5. All chemicals, sharps, etc. must be disposed of properly. If you are not sure, ask.
6. Women who are pregnant need to discuss the course with me because of potential and known
mutagenic and teratogenic chemicals involved in some experiments.
7. Come to lab prepared!
Clean-up: At the end of the lab period, all reusable labware needs to be cleaned, rinsed with dH 2O and allowed to
dry. All equipment should be returned to their designated location.
LDH Research Presentations: The week of Nov. 15th we will be conducting an in depth seminar on the sequence,
structure, function, and catalysis of Lactate Dehydrogenase (LDH). I will assign topics to be researched to several
groups in class mid-September. Each group will then conduct library research on their topic and present it in lab the
week of Nov. 12. Each group must have at least 3 primary sources for their data (i.e. journal articles, book
enteries, etc.) If you simply take things off the WWW you will lose significant points. The idea here is to
introduce you to a full investigation of an enzyme and teach you the tools needed to perform library research. Each
group presentation will be approx. 25-30 min long, and groups will consist of 3-4 members.
Assignments to be turned in: Lab assignments will consist of the following:
1. The prelab questions will be turned in at the beginning of that weeks lab.
2. Your notebook pages will be turned in at the beginning of the next lab period stapled to your lab report.
3. The preprinted lab analysis sheets from the lab manual, as well as any assigned problems, will also be
turned in at the beginning of the next lab period.
4. If you do not hand in assignments at the beginning of the lab, it is late and it will be assessed a late penalty.
5. I will not accept late lab reports after one week.
Laboratory Grading:
Prelab, Analysis Sheets and
Laboratory notebook
LDH Research Presentation
Total
300 points
60 points
360 points
* I retain the right to change this syllabus, as I deem necessary at any time during the semester.
One final note: I have been in the lab long enough to know that things do not always go as planned when
performing an experiment (i.e. you drop the test tube containing your precious enzyme, etc.). I will allow for
unforeseeable error, however, if your errors are due to an obvious lack of preparation, leniency will not be
forthcoming. In addition, I have upgraded our biochem lab to contain lots of newer “state-of-the-art” equipment.
My goal is to teach you many of the common everyday practices done in real industrial or academic research labs
using the “tools of the trade”. Please treat the equipment with respect.
Student Accommodations and Support Services:
In compliance with Lake Superior State University policy and equal access laws, disability-related accommodations
or services are available. Students are to meet with the professor in a timely manner, preferably the first week of
class, to discuss their disability related needs. Students are required to register with the Office of Student
Accommodations and Support Services (OSASS) for disability verification and for determination of reasonable
academic accommodations. OSASS is located in the KJS Library, Office 144, Ext. 7559.