BioC 4025BIOCHEMISTRY LABORATORY
*Syllabus Only*
BIOC 4025
“Laboratory Methods in Biochemistry Manual”
January 20, 2015 – May 6, 2015
Lab: Tues or Thurs, 8:15am, 1:15pm, or 5:20pm
2-126 MCB, Minneapolis Campus
Lecture: Monday 4:40 pm
Room: 3-120 MCB
Instructor: Professor Alex J. Lange, Department of Biochemistry, Molecular Biology and Biophysics. , Tel. 6-4502
BIOC 4025
Spring Semester 2015
Professor Alex Lange
Instructor
Instructor:Professor Alex Lange
Dept. of Biochemistry, Molecular Biology and Biophysics
e-mail:
7-136 MCB Building, Minneapolis
Teaching Assistants:
Aaron Edmund
Chao Li-13
Sujin Yeom
Required Book:
Laboratory Methods in Biochemistry Manual This course packet is available weekly on Moodle. You are advised to download and compile the weekly installments. We are in the continual process of editing this manual, and will try to stay a few weeks ahead of you in making edits. Suggestions on how to improve the manual are welcome, if constructive.
Supplementary reference (several are available in the Lab):
- Lehninger- Principles of Biochemistry: Nelson and Cox, Worth Publishing (6th edition is the newest) Or any other biochemistry textbook
Syllabus: BioC 4025: Laboratory in Biochemistry
Spring 2015
Course Goals: Laboratory experience in protein expression, purification and characterization; an appreciation for the role of protein expression and purification in modern (G4) life.
Topics: Buffers and solutions, protein (lactate dehydrogenase) purification, protein electrophoresis, protein expression using recombinant technology, enzyme characterization using kinetic and immunochemical methods.
Instructor:
Alex Lange, e-mail: , phone: 612-626-4502. Office location: MCB 7-136. Office hrs: Will be available Mondays before lecture in the Molecular and Cellular Biology (MCB) Bldg. outside of the class room 3-120.
Teaching Assistants:
TA Name / Email address / Office Hours / Section / TimesChao Li / / 9:30- 10:30 am Friday
MCB 2-126 / 5 & 7 / Thurs 1:15pm
Thurs 5:20pm
Aaron Edmond / / 10-11 am Monday
MCB 2-126 / 3 & 6 / Tues 1:15pm
Tues 5:20pm
Sujin Yeom / / 11:30-12:30
Wednesday
240H Gortner Hall (St. Paul) / 2 & 4 / Tues 8:15am
Thurs 8:15am
Section 1 / Monday (Lecture) All students
Section 2 / Tues 8:15 am 16 students (max)
Section 3 / Tues 1:15 pm 16 students (max)
Section 4 / Thurs 8:15 am 16 students (max)
Section 5 / Thurs 1:15 pm 16 students (max)
Section 6 / Tues 5:20 pm 16 students (max)
Section 7 / Thurs 5:20 pm 16 students (max)
Check with TA to confirm office hours. You ca go to any TA for help.
Laboratory coordinator:
Barbara Pinch, Room 2-132 MCB (office/prep room), e-mail: , phone: 612-625-4282.
Prerequisites: BioC 3021 (Biochemistry) or BioC 4331 (Biochemistry I) or Biol 3021 (Biochemistry). Contact instructor for exceptions.
Text (Lab manual): A Laboratory Manual (Laboratory Methods in Biochemistry Manual) will be provided on MOODLE on a weekly basis. The course is keyed to the week number(WEEK 1, WEEK 2, etc.) Week number matches Lab number.
Supplement: Supplementary materials will be distributed as needed. Since we are editing manual, hopefully there will not be a great deal of supplemental material.
Laboratory Notebook:A bound, graph-ruled laboratory notebook is required. Examples are U of MN No. 20775 (96 pp.) or Dennison 73333 53110 (96 pp). No loose-leaf or spiral bound notebooks.
Course web site: login via MOODLE: syllabus, schedule, Lab Manual, lecture slides, example exams, current grades, and additional materials as needed. No handouts will be given out for lectures. Students are advised to print out the posted lab manual and lecture handouts from the web site.
Lectures: (Section 1, all students) Mondays at 3:35-4:25 pm in MCB 3-120. These are important because they will cover what you are doing that week in the lab.
Laboratory: Tuesday and Thursday in MCB 2-126. Laboratory start times are shown in the table above. There are 6 lab sections. Tues morning, section 2; Tues afternoon, section 3; Tues evening, section 6; Thurs morning, section 4; Thurs afternoon, section 5; and Thurs evening, section 7. The lecture is section 1 (all students).
Grading Scheme:Points
Lecture
Quizzes (LecQ, best 5 out of 6, 10 pts each)50(8.3%)
Midterm & final exams (MTE-80 pts., FE-80-pts.)160(27%)
Biochem Q and A (BQA - weekly ½ page referenced
reports on biochemical question of your choosing
(Ex. How does aspirin work, biochemical mechanism?)
(BQA1[4 ]-20 pts., BQA2 [4]-20 pts.)40(6.7%) ______
Lecture Subtotal250(42%)
Laboratory
Prelab quest., notebook (PreLab, best 10 out of 11)75(12.5%)
Punctual arrival, cooperation & cleanup (PACC)25(4.2%)
Lab reports & questions (LabR, best 12 out of 13,150(25%)
12.5 pts. each)
Large lab report (LLR)100(16.7%)
______
Laboratory Subtotal350 (58%)
______
Grand Total600(100%)
Course Description
This biochemistry laboratory course is designed to give students hands-on experience performing common strategies and techniques used in modern biochemistry, as well as the background information needed to understand what kind of information can be obtained by using them. Because of the dual nature of this course, a portion of the laboratory time will be spent on lectures explaining the theory behind the techniques being used as well as practical aspects of experimental design. In addition, readings will be assigned that explain the history and principles behind some of the techniques used.
Course Objectives
- Students will be able to successfully perform some basic techniques used in modern biochemistry.
- Students will be able to interpret data from their experiments.
- Students will be able to design protein purification and characterization experiments using the techniques learned in the lab.
- Students will be able to use computer-based sequence analysis software and to find nucleic acid and protein sequence information using the Internet.
Learning Goals
1. Foundational Knowledge
Be able to explain and discuss key ideas regarding pH and buffers, strategies in protein purification and characterization, different types of chromatography and electrophoresis methods. Be able to identify unsolved scientific problems related to protein purification and characterization.
2. Application Goals
Be able to critically evaluate a protein purification – does it achieve its goals of purity, cost, safety? Be able to critically evaluate a protein characterization – does it establish the purity and identity of the protein? Be able to evaluate a proposed experimental procedure for safety issues. Be able to work safely in a laboratory
3. Integration
Be able to identify where proteins and protein purification affect our daily life. Be able to identify current society issues involving protein purification and characterization. Be able to identify where advances in protein purification and characterization have created business opportunities. Be able to identify ethical issues created by protein purification and characterization technologies.
Grading Guidelines and Course Policies
In lecture quizzes (50 pts., best 5 out of 6, 10 pts. each)
Random lecture classes will include a quiz. The possible grades are 0-10 for each. The best 5 quizzes will go toward your grade. There is no opportunity to make these up if you miss them. The quiz will test your understanding of assigned reading material, laboratory experiments, and lecture material.
In lecture midterm exam (March 9, 2015) and final exam (May 4, 2015) (50 min for each, 80 pts. each, 160 pts. total)
These closed book exams consist of multiple choice, short answers, and simple problems that cover understanding of the laboratory experiments and lecture material. Calculators may be used. If you miss an exam and have an excused absence, then you must make arrangements with the instructor to take a make-up exam. The makeup exam may have a different format (e.g. all essay). Alternately, for an excused absence you may be able to take midterm exam early. Final exams may not be taken early. All exam time/date changes must be in writing (e-mail OK). Calculators may be used, however no external communication is allowed during the examinations.
Biochem Q and As (first 4 [20 pts.], second 4 [20 pts.] = 40 pts. total)
A Biochem Q and A is a written record of your reflections on how biochemistry relates to things of interest to you. Can you relate what you are learning to the world you live in? Pose a question on something related to biochemistry that you don’t understand and try to find the answer to it from the literature search you do. You can take things from current events of the day. All sources are allowed, but put your reports in your own words. Primary sources can be used to back up web sources. Cite your sources.
Part 1. Write a weekly short report, starting in week 2, you must write at least a single spaced ½ page report every week. The first 4 BQAs will be turned in on March 2nd, 2015,before or after lecture.
Part 2. Continue weekly reports as above. The second 4 entries will be turned on April20th, 2015, before or after lecture.
These will be assessed based on the student asking questions for which biochemistry knowledge will give him/her a better understanding of how things work (or don’t work) in the world.
A reference for each report will be required.
Prelab (75 pts, best 10 out of 11 labs at 7.5 pts each excluding the first one)
The prelab has three components that are listed below:
All three of these components must be completed before you come to lab.
Component 1: Assigned prelab questions (2.5 pts.)
These are at the beginning of the lab procedures for each week, must be answered in your notebook. You may photocopy the questions from the lab manual and paste them into your notebook (ANSWERS MUST BE WRITTEN IN YOUR LAB NOTEBOOK).
Component 2: Your planned experimental procedure in your notebook (2.5 pts)
1. Title of the experiment and the date on a new page.
2. Objective: One or two sentences stating the purpose of the experiment.
3. Materials: any reagents, chemicals, equipment, etc. for the experiment. The composition of all buffers should be included or a page number given for a notebook entry that contains the buffer composition and the calculations made in preparing solutions.
4. Procedures: outline or flow sheet of the procedure based on the lab manual. Tables are also useful for experiments with multiple variables. A checklist of things to add/complete is useful. You may not tape photocopies of procedure overheads into your notebook. You must make a plan for yourself so you know what you are doing.
Component 3: Lab notebook entries below (5. results and 6 conclusion/summary.) from the previous week). (2.5 pts)
5. Results: Record all data taken, gel photos, printouts, etc., all calculations, analyzed data, and remarks about how the experiments proceed. Note any deviations of the actual procedure from the preliminary protocol. A lab book should provide all the information needed for someone to repeat your methods and results.
6. Conclusions/Summary: briefly summarize your results and state your conclusions. If the experiment didn’t work, hypothesize what went wrong and what will you do next time to try to trouble shoot?
Note: 3 parts to the prelab, 2.5 pts each
Punctual arrival to laboratory, co-operation & clean up (everyone starts with 25 pts)
Failure to do these things will result in an erosion of these points. Also, you must be dressed in long pants with closed-toe shoes.
During lab:
Clean up any spills or broken glass (broken should be put in the “Broken Glass” disposal box.).
Missing a lab (only with a written, valid excuse, e.g., illness, grad school interview):
Check with the TA for another section and get permission to attend and do the lab in another section. It must be in the same week as the lab set up will be different the next week. You are allowed only one excused lab.
You cannot switch labs without a valid reason.
Switching sections – It is difficult to switch sections, but if the excusable occasion arises, you will be allowed to switch only once.
Missing 2 unexcused labs will result in being dropped from the course.
The best thing you can do is be there for all the labs. The lab experiments are sequential and if interrupted, you do not have what you need to go forward. Also, if you are not conscientious, your lab partner will suffer, remember, you are a team.
Lab reports and assigned questions (150 pts, best 12 out of 13)
General:
Write your answers using a computer and hand in paper copies. Check with your TAs for any changes in format.
Numbers without units are incorrect (unless it is a unitless number, e.g. pH, absorbance).
All graphs must have axis labels with units and scales.
Show your work for all calculations.
Your teaching assistant will provide detailed grading criteria.
Large lab report (to be turned in at the end of the semester): This is a cumulative report where you report your semester’s work, which involves the isolation, expression, purification and characterization of the enzyme LDH. It is worth 100 pts., or 1/6 of your grade. You will be given more information and instructions on the large lab report during the course.
General Policies
Late work policy: loss of 10% of max score per 24 h or part thereof including weekends and holidays. Example: Five points will be deducted from an assignment worth 50 points that is 12 h late.
Basis for an incomplete: If you miss three or more labs due to documented illness or extraordinary circumstances, you will get a grade of "I” or Incomplete. Incompletes are not given because a student is earning a low grade.Before an ‘I’ grade is given, the instructor and student must fill out an Incomplete Contract. To complete the course, the entire course must be repeated. ( which outlines the conditions for making up the missed laboratories and other work. "I" grades automatically lapse to ‘F’s at the end of the next semester of a student's registration, unless an instructor submits a change of grade.
Changes of grade: Only requests in writing (e-mail OK) will be considered within two weeks of the grade return date. State the reasons that your grade should be changed. The instructor or TA will consider your request, its fairness to the other members in the class, and give an answer in two days. If you are not satisfied, you may then contact the Student Dispute Resolution Center (SDRC) in 107 Eddy Hall (625-5900) for assistance.
Extra work: Students are not permitted to submit extra work to raise their grade.
Scholastic misconduct is broadly defined as "any act that violates the right of another student in academic work or that involves misrepresentation of your own work. Scholastic dishonesty includes, (but is not necessarily limited to): cheating on assignments or examinations; plagiarizing, which means misrepresenting as your own work any part of work done by another; submitting the same paper, or substantially similar papers, to meet the requirements of more than one course without the approval and consent of all instructors concerned; depriving another student of necessary course materials; or interfering with another student's work." If you are not sure, ask your instructor or TA or check the student code at: Suspected scholastic misconduct will be dealt with through university procedures for academic dishonesty ( Plagiarism also includes copying directly without attribution from a book, journal article, the lab manual or the internet. Discussing ideas, procedures, and interpretations is encouraged. You must write your own lab reports and QAs. Info on distinguishing between plagiarism and legitimate use and citation of someone else's work:
E-mail course notices: Course information will occasionally be sent out by email to your assigned “” address. Please check your umn.edu mailbox daily. Don’t forward your umn.edu mail to another account (e.g. hotmail or yahoo), as these accounts can fill up and reject important messages.
Accommodations for student with disabilities: If you have a disability that might hinder full participation class activities, contact the instructor. Additional information is available from Disability Services in 230 Gateway (V/TTY) 624-4037.
How to get an “A” in this course
A = 93 to 100, A- = 90-92. The course will not be curved.
1. Keep up with the course schedule.
Attend each class and lab and arrive on time, or it will cost you points.
Arrive prepared: reading completed, prelab questions done, lab notebook filled out for the last week’s experiment and for the current experiment.
Clean up after yourself in the lab.
Hand in your lab reports and learning profiles on time.
2. Think about the course and its implications on society.
Think while you work in the lab. Why are you doing each step? What do you expect to happen? What could go wrong? On the molecular level, what is happening at each step?
Make entries in your learning portfolio each week. Think about how proteins influence your life and society. Notice protein issues in the news.
Take notes in class. Clarify things you are not sure about by asking questions.
3. Write excellent lab reports.
Reports should be clearly written and demonstrate that you understand not only what you did and why, but also the implications of the experiments in other situations. It is not essential that the lab experiments succeed to get a good grade, but it is essential that you demonstrate mastery of the concepts and implication of the experiment.
4. Do well (≥90%) on the midterm and final exam.
If you are not on track to get the grade you expect in within the first three weeks, you must change your approach to the course. Contact your TA or the instructor. Student Expectations: As a student in this course, you are expected to take an active role in your learning.
- You are expected to attend every class, and to arrive on time and not leave early.
- You should be prepared for each lecture by reading the assigned material. You should take good lecture notes and use them to make sure you understand all of the concepts covered in class.
- You should ask questions in lecture to help clarify concepts.
- You should participate actively in the discussion sessions.
- You should adhere to the University of Minnesota Student Conduct Code found at:
The university policies and where to find them on the web follows:
The University utilizes plus and minus grading on a 4.000 cumulative grade point scale in accordance with the following:
A / 4.0 - Represents achievement that is outstanding relative to the level necessary to meet course requirementsB / 3.0 - Represents achievement that is significantly above the level necessary to meet course requirements
C / 2.0 - Represents achievement that meets the course requirements in every respect
D / 1.0 - Represents achievement that is worthy of credit even though it fails to meet fully the course requirements
S / Represents achievement that is satisfactory, which is equivalent to a C- or better.
For additional information, please refer to: