Introduction to Biochemistry 325
Dr. Carl W. Vermeulen
(click his name for his biographical sketch)
Office = Camp 303; Lab = Camp 310; Phone = 757-508-0852; Email = ecoligist@yahoo.com
Office hours = Tues 10-11; Wed 10-noon; Thurs 10-11
Text: Campbell, Mary K., and Shawn O Farrell. "Biochemistry" editions 4 or 5
Lectures and labs are outlined in Dr. V's website:
www.science-projects.com/CB/325Index.html
CATALOG DESCRIPTION
Chem 325 - Introduction to Biochemistry. A study of the behavior of organic molecules which are significant in biological systems; structure-property relationships with biochemical systems are emphasized. Topics in biotechnology are included in both the lecture and laboratory. Three hours of lecture and one three-hour laboratory per week. Credit: 4 hours (Spring). Prerequisite: Chemistry 275 (first semester of organic chemistry)
COURSE GOALS
The purpose or educational outcome of this upper-division lecture/laboratory course is to give both those students who intend to continue in biochemistry and those from other disciplines wishing an expanded science education an in-depth introduction to this mushrooming field of Molecular Biology or Applied Organic Chemistry (depending on the student's point of view).
GRADING: This will be via twelve approximately weekly examinations in the laboratory with the lowest two grades dropped (a 12-2 policy). The undroppable final exam will count as a double exam. The grade will then be determined by the normal distribution curve with the average being defined as a curved 85, and each standard deviation will be a corresponding letter grade (all 80's = B, etc.). Furthermore, if you are fortunate to obtain a curved grade of 93 or higher, you will have the option of taking a "curved" 90 on the next quiz, OR taking the next quiz at your own risk. If absence is caused by matters beyond the student's control - hospitalization, death in the family, etc., the 12-2 policy will be prorated (e.g.: if 10 quizzes are taken, 1.67 of the lowest will be dropped). There shall ALSO be further opportunities to gain points through homework, brilliant classroom comments, and constructive criticism of the course. ADDITIONAL grading parameters are given on the laboratory introduction page.
Oral and Written Presentation Requirement Due: first presentation the week after Spring Break; second presentation the last week of classes. Why is all this emphasis on writing and speaking? Because it has become a lost art what with multiple choice exams and computer short-answer surveys. But when you go for a job interview - one of the most important things you will do in your life - you will have to talk (you're making your first impression) and then write.
As mentioned on another page, your writing will be as a group effort and will follow scientific-journal style. Your individual TALKS will be of three sorts - a 15 second talk, a minute-long talk, and a five minute talk with whatever visual aids you want. The subject will be the same for all of them - only the lengths will be different. Why three different lengths? So you will be prepared for whatever encounter you have with your prospective employer. Let me give you a scenario taken from the archives of a training course for pharmaceutical reps to doctors' offices. I will just put it more personally as you are being interviewed for either graduate or medical school.
You have an appointment at 1:30 p.m. with Dr. Smith in room 310, and you show up on time, of course. Dr. Smith calls you in and starts asking you questions, and then notes that you have done a research project in college. "Would you tell me about it?"
No more than you open your mouth the intercom requests Dr. Smith for an emergency meeting immediately.
Smith: "Can you tell me about it in just a few words?"
Here comes your 15 second speech! It is so enticing that Smith wants to hear more. You are invited to tag along on the way to the meeting - about a minute's walk - and tell Smith more about it - your 1-minute speech! At the door Smith tells you to return to room 310 at 3 p.m., which you do because your talks have really "hooked" Smith's interest.
At 3 p.m., Smith hears more about what you have to say and also looks through the photos and other illustrations you have. "How would you like to be one of the three presenters at tomorrow's brown-bag lunch, where interested people in my department come to listen to some of the latest research. I think they'll be interested to hear what you have to say." You can see your 15-minute talk being presented as a slide or transparency talk. Even more, you know that if you give a clear presentation, you will be more than merely accepted - perhaps invited to join the program!
First you want to work on your long talk with illustrations. It will, of course, come in three parts - you first tell them what you want to tell them; then you tell them; and finally you tell them what you told them. (If you want this spelled out more fully: "I want to tell you about.... Now let me tell you about it in detail... Therefore you now see that...is very important."
In this long form, it is always important to have the opening sentence be your hook or hooker - a statement that so captures their attention that they want to know more and will stay awake to hear you out. This might be the hardest part about making up any of the three talks - as all need to include the hook. The 15 second talk will probably be nothing but the hook and the results in the briefest form.
When the instructor feels you have composed your three parts with finesse, you will be presented to the class for comments and get your grade for accomplishing the task.
What will you topic be? It would be preferable if it were on your research project, if you have done one. If you have not done one up to now, perhaps you could start it as part of this course, or you might want to use a take-off on one of the lab exercises we shall do this semester.
What might be some examples:
You are maturing students in the sciences, and shall be given much more latitude to work on the above sorts of mini-projects. Your practice in talking and writing about these will make life MUCH easier for you when the time really counts - when you must describe to your hoped-for employer the work you have done previously.
(based on lab work)
Biochemistry 325
| L E C T U R E S Quizzes and Tests will be given during lab time | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Lecture # | Date Text pages 5th ed Text pages 4th ed | Topic(s) | Page | ||||||
| 1 | January 10 (in lab) | Introduction to the course Nobel Laureates in Biochemistry Research interests of the instructor | 1 2 3 | ||||||
| 2 | January 11 | Control [coarse] mechanisms - the Lac-Operon | 5 | ||||||
| 3 | January 16 131-139 | General enzymology; active sites; molecular ecology | 10 | ||||||
| 4 | January 18 139-155 | Kinetics I: Michaelis-Menton Theory | 15 | ||||||
| 5 | January 23 156-183 | Kinetics II: Fine control mechanisms | 20 | ||||||
| 6 | January 25 463- |
| 25 26 | ||||||
| 7 | January 30 486 | Glycolysis B: The EMP continued | 30 | ||||||
| 7 | February 01 486 | The Entner-Douderoff Pathway | 33 | ||||||
| 8 | February 06 515-518 | The Korkes-Gunsälus Intermediate Pathway | 35 | ||||||
| 9 | February 08 | Glycolytic Inhibitors; Poisson Distribution | 40 | ||||||
| 10 | February 13 540-567 | Electron Transport and Oxidative Phosphorylation | 45 | ||||||
| 11 | February 15 | Membranes and Transport (goes with the LPS SDS-PAGE lab) | 50 | ||||||
| 12 | February 20 511-539 | Krebs Cycle; P/O; inhibitors, etc. | 55 | ||||||
| 13 | February 22 | Energetics of the above pathways | 60 | ||||||
| 14 | February 27 504-510 | Pentose Shunt [aka: Hexose monophosphate shunt, HMS] | 65 | ||||||
| 15 | March 01 434-447 |
| 70 75 76 | ||||||
| 16 | March 06 448-462;487-494 | Carbohydrates II: Polymers The Glycogen Cycle Hormal Control of the Glycogen Cycle | 80 | ||||||
| 17 | March 20 | Proteins IIIA: isolation and purification procedures | 85 | ||||||
| 18 | March 22 80-112 | Proteins IV: structural analysis in vitro Synthesis of the Peptide Bond | 90 91 | ||||||
| 19 | March 27 58-72 | Proteins I: amino acids, chemical tests, structural classification | 95 | ||||||
| 20 | March 29 122-130 | Proteins II: degradation (chemical and enzymatic) Practice Problem | 100 101 | ||||||
| 21 | April 03 629-648 | The Nitrogen Pool (Ammonium fixation & Transamination) | 105 | ||||||
| Here a placement quiz will be given to ascertain which of the following may be skipped due the students' having had genetics. | |||||||||
| 22 | April 03 | In vivo Protein Synthesis | 110 | ||||||
| 23 | April 05 568-586 | Fat and Terpene Syntheses | 115 | ||||||
| 24 | April 10 586-603 | Other Lipids | 120 | ||||||
| 25 | April 12 648-656 | Nucleotide biosynthesis | 125 | ||||||
| 26 | April 17 | Protein biosynthesis | 130 | ||||||
| 27 | April 19 656 | Nucleoside catabolism | 135 | ||||||
| 28 | April 24 657-661 | Nucleic acid biosyntheses | 140 | ||||||
| 29 | April 26 | Vitamin Survey | 145 | ||||||
| 30 | May 01 | Carbon-carbon bond formation review | 150 | ||||||
| 31 | May 02 | Immunology | 155 | ||||||
| 32 | May 02 | Help Session for exam in lab | |||||||
| L A B O R A T O R Y | |||
|---|---|---|---|
| Labs will usually begin with a quiz on previous and current work. There is no published lab manual; handouts will be provided on-line. | |||
| # | Date | Subject | Page |
| 1 | Jan 10 | Intro to course Preparation of source material - 1 Mission Lac-Operon Basic Bacteriological Preparations | 400 401 402 |
| 2 | Jan 17 | Preparation of source material - 2 Looking for catalase and lactase in bacteria and selected eukaryotes Learning how to use substrate analogs and the spectrophotometer In vitro lactase inhibition, In vivo lactase inhibition | 410 411 412 413 |
| 3 | Jan 24 | Qualitative and Quantitative Methods in Protein Chemistry | 420 |
| 4 | Jan 31 | Paper chromatography of amino acids and their derivatives amino acids, proteins and enymatic activities with unknowns! RF values of amino acids RF values of DNP-amino acid derivatives | 430 436 437 |
| 5 | Feb 07 | Qualitative and Quantitative Methods in Carbohydrate Chemistry using chromatographic and other techniques such as optical rotation and chemical tests | 440 |
| 6 | Feb 14 | A Study of the Effects of Fever on E. coli Lipopolysaccharide Set up and preparation | 450 |
| 7 | Feb 21 | SDS-PAGE and Development of E. coli LPS (detergent augmented polyacrylamide gel electrophoresis and silver staining of gels) | 460 |
| 8 | Feb 28 | Intro quiz to Photosynthesis Photosynthesis Lab A Study of Light Extension #1 Extension #2 | 470 471 472 473 |
| 9 | Mar 07 | Metabolism - 1 Optimization of Growth | 480 |
| 10 | Mar21 | Metabolism - 2 Inhibitors | 490 |
| 11 | Mar 28 | ETOP and inhibitors | 500 |
| 12 | Apr 04 | Isolation of DNA and RNA Investigation of some of their chemical and physical properties. (More sophisticated exercises are done in Genetics and will not be done here.) | 510 |
| 13 | Apr 11 | Determination of Kinetics Constants, KM, Vmax of either lactase or catalase. | 520 |
| 14 | Apr 18 | Lipid Biochemistry | 530 |
| 15 | Apr 25 | Mini-Research Projects | 530 |
| 16 | May 02 | Help Session for Final Exam | |
| FINAL EXAM STUFF | |
|---|---|
| I T E M | Page |
| My sketches of the structures of GLUCOSE, ATP, NAD+/NADH | 800 |
| My list of Carbon-Carbon bond formations and breakings | 805 |
| My list of the vitamins covered in this course and their molecular points of action | 810 |
| My list of techniques I've learned in this course. | 815 |