BCH 4053L
Spring 2004

Dr. Michael Blaber

Lecture: Tue 1:00 - 1:50 p.m. HTL 213
Lab:  Tue & Thu 2:00 - 5:00 p.m. HTL 407

Course URL:
http://wine1.sb.fsu.edu/bch4053L/

 

Syllabus

 Description/Objectives

General biochemistry laboratory, covering methods of electrophoresis, chromatography, cell fractionation, and enzyme assays, ligand interactions, and recombinant DNA technology. 3 units of credit.

Lecture 1 hour per week, lab 6 hours per week. Most experiments are designed to be completed comfortably within a 3 hr. period by a well prepared student.  A few experiments are more demanding and may require more than three hours to complete.  You will be given advance notice of experiments that are most likely to extend past the normal period time.

Text: Fundamental Laboratory Approaches for Biochemistry and Biotechnology. Ninfa and Ballou. Fitzgerald Science Press, Inc.
ISBN: 1-891786-00-8

Web resource: http://wine1.sb.fsu.edu/bch4053L/
Online syllabus: http://wine1.sb.fsu.edu/bch4053L/syllabus/syllabus.htm

Students completing this course should be able to:

·         Perform a variety of common biochemical experiments with adherence to accepted standards of practice, accuracy and safety

·         Perform a several common biochemical assays including protein and DNA quantitation, enzyme kinetic assays

·         Perform standard biochemical separation techniques, including chromatography and electrophoresis

·         Analyze the strengths of interactions between biological macromolecules and ligands

·         Perform basic techniques of recombinant DNA technology including isolation and restriction endonuclease analysis of DNA, and detection of an expressed protein;

·         Become familiar with basic computational aspects of data analysis

·         Maintain records in a laboratory notebook and prepare research reports following professional standards

·         Demonstrate knowledge of accepted practices in the biochemistry laboratory, and of principles underlying laboratory experiments

Requirements

Prerequisite: CHM 3120C.  Co-requisite: BCH 4053.

Grading/Evaluation

The grade for the course will be based on the following:

  • Written lab reports (200 points possible)
  • Lab notebooks (25 points possible)
  • Lab quizzes (40 points possible)

Written Lab Reports

Each experiment (see schedule below) requires a written lab report.  The lab report contains the following sections:

1.       Title

2.       Introduction

3.       Materials and Methods

4.       Results

5.       Discussion

6.       References

An important part of this laboratory course is to develop the student's ability to prepare a formal scientific written report.  Details of these sections will be covered in lecture, however, a brief description follows:

·         Title - a single sentence that states the purpose of the experiment

·         Introduction - one or more paragraphs that explain the purpose of the experiment, and provide any relevant background information so that the reader is prepared to follow the narrative of the report

·         Materials and Methods - a detailed "recipe", describing instrumentation, materials and supplies, and procedures used in performing the experiment.  The "M&M" section is detailed enough so that the experiment can be repeated (and the results confirmed) by others

·         Results - statements of fact regarding the data collected, with associated errors or deviations (e.g. all relevant values and standard deviations)

·         Discussion - an interpretation of the results, and a discussion of its meaning, including a discussion of error (where relevant).

Reports must follow the following style convention:

·         Must be typed (i.e. printed) and not handwritten

·         Double spaced, except for tables, which are to be single spaced

·         12 point font size, Times Roman for all text but title, which will be 14 point bold.  Section headings are 12 point bold.

·         1" margins top, bottom, left and right

·         Sections identified in bold

·         Student name provided below title, along with course and lab number and date

AN EXAMPLE LAB REPORT CAN BE FOUND BY CLICKING HERE (NOTE: PDF FILE)

There are a total of 24 labs currently scheduled (this is subject to change, however).  Each lab report will be graded on a 10 point system:

·         Correctly following the required format (see above) for lab reports (i.e. relevant sections, font and spacing) (2 points)

·         Each section (Introduction, M&M, Results and Discussion) is worth 2 points and focus is placed upon the following:

o        The introduction clearly explains the purpose of the experiment, and does not information that should go in other sections

o        The M&M section provides appropriate detail so that the experiment can be repeated by others.  No other information should go here (i.e. no results)

o        The Results section includes data, and does not include discussion of the meaning of the data.  Appropriate tables or figures are used.

o        The Discussion section provides an appropriate narrative explaining what the results mean, and discuss potential sources of error

LAB REPORTS ARE DUE FIRST THING MONDAY MORNING AFTER THE LAB IS GIVEN, AND ARE TO BE TURNED IN TO THE LAB TA'S AT A TIME AND PLACE TO BE ANNOUNCED. 

·         LATE REPORTS WILL NOT BE ACCEPTED AND WILL BE GRADED 0 (ZERO). 

·         ALTHOUGH THE LABS THEMSELVES MAY BE PERFORMED IN GROUPS, LAB REPORTS ARE INDIVIDUAL EFFORTS AND MAY NOT BE COPIED FROM ANOTHER STUDENT. 

·         IF DUPLICATE REPORTS ARE IDENTIFIED, BOTH PARTIES WILL RECEIVE ZERO FOR THAT LAB.

The lab reports will comprise 200 points total for the course.  Thus, the top scores for only 20 labs will count, and the remaining scores will be dropped.

Lab Notebooks

Students are expected to keep a laboratory notebook.  The laboratory notebook is different from the written lab report.  The laboratory notebook is a student's "working" lab book and has several requirements.  Primarily, the purpose of the notebook is to allow someone, at a later date, to see exactly how the experiment was performed and what results were obtained.  The following procedures must be followed with regard to the laboratory notebook.  Laboratory notebooks (for this course) do not contain discussion or conclusions.

  • The first 2 pages must be reserved for a table of contents (i.e. at least 24 blank lines for listing the labs and the relevant page numbers).  The table of contents is filled in as the lab experiments are performed.
  • Notes must be taken in ink.  NO PENCIL.
  • Pages must be numbered sequentially, and under no circumstances are pages to be ripped out or removed.
  • For each experiment, the student must do the following:
    • Starting on a new page, provide the date
    • State the purpose of the experiment
    • Show all calculations
    • Write down all procedures followed
    • Write down all data & results collected
  • The lab notebook must not contain loose scraps of paper.  Any supplementary information or material (such as printouts from instrumentation, photographs, etc.) must either be copied into the notebook, or securely fastened with glue, tape or staples.

Laboratory notebooks will be turned in and graded at the end of the course.  The notebooks will be graded out of a maximum of 25 points

  • Table of contents is accurate (5 points) (-1 for each error in table of contents)
  • Pages are sequentially numbered with no missing pages (5 points) (-1 point for each missing page or misnumbering)
  • Each lab has the date and statement of purpose (5 points) (note: -1 point for each missing date or statement of purpose)
  • All data is written in the notebooks in ink, or firmly attached (no loose scraps of paper, no pencil). (5 points)  (note: -1 point for each lab written in pencil, or for each loose piece of paper)
  • Handwriting is legible (5 points) - note handwriting does not have to be pretty, but a reader does have to be able to read it, and follow the procedure.  (-1 point for any lab where the protocol is impossible to decipher - either due to poor handwriting or disorganized notes)
  • 20 labs reports will be graded (see above) therefore, any missing labs beyond a total of 20 will result in -5 points per missing lab

Lab quizzes

At the beginning of each lab there will be a short quiz.  The quiz will start promptly at the beginning of the class, and last no more than 10 minutes.  There are no make-up quizzes for any reason, this includes being late for lab.  Each quiz will be worth 2 points, and 20 quizzes will count (for a total of 40 points).

Grade scale

There are a maximum of 265 points available in the course (200 lab reports, 25 lab notebook, 40 lab quizzes) and the grading is expected to follow a standard percentage scale:

%

Grade

Points

³ 93%

A

³ 246

³ 90%

A-

³ 238

³ 87%

B+

³ 230

³ 83%

B

³ 220

³ 80%

B-

³ 212

³ 77%

C+

³ 204

³ 73%

C

³ 193

³ 70%

C-

³ 185

³ 60%

D

³ 159

<60%

F

< 159

Laboratory Safety and Practices

    1. Eating and smoking are not permitted in the laboratory.
    2. Use of cellular phones will not be permitted.  Please turn off cell phones before entering the laboratory.
    3. Dress: You will be asked to leave if you are not dressed appropriately:
      • Safety glasses or goggles must be worn at all times. 
      • Shoes (i.e. closed toes), not sandals, are required.
      • Students should be aware that laboratory spills and splashes can, and do, occur, so students are strongly advised to wear a laboratory coat or apron.
      • Short shorts or short skirts are not allowed unless covered completely.  No bare midriffs.
    1. Accidents or injuries:  Accidents and injuries must be reported to the TAs, however minor they may seem at the time.
    2. Spills:   Spills not involving personal danger should FIRST BE CONTAINED with a sponge or paper towels, then reported to the TA.  Spills must be cleaned up as soon as possible according to the TA’s instructions.  PROMPTLY CLEAN UP ALL SPILLS.
    3. Personal chemical exposure: The best response if your skin comes in contact with a potentially harmful chemical is generally to WASH THE AFFECTED AREA THOROUGHLY WITH SOAPY WATER (if readily available) or plain tap water immediately.   There should be a wash bottle of soapy water on each bench.  Notify the TA for a treatment more specific to the chemical as soon as practical after you wash the affected area. 
      • Minimize risk of contact to hands and wrists by wearing gloves while working directly with potentially hazardous chemicals.  Disposable gloves are available in the lab.  Be sure to ask the TA if gloves in your size are not available, or if you have allergy problems with the gloves provided.  Do not rub your eyes or other areas unless you are confident your hands are clean.
      • When you leave the laboratory it is safest to assume that some chemicals might be on your hands.  Wash your hands well before leaving so that you do not spread chemicals to other body areas or contaminate food.
      • Shower, eye wash and other emergency equipment.  There is a shower available in the room to be used in cases of extreme chemical contact.  There is also an eye wash stand to be used if chemicals are splashed or rubbed into the eyes.  Make a mental record of locations of fire extinguishers and other safety equipment.  These will be pointed out during the first session.
      • Wear appropriate protection.  Avoid direct chemical contact by wearing appropriate clothing, latex gloves and eye protection.   We are required to insist that you WEAR SAFETY GLASSES AT ALL TIMES in the laboratory.   Your instructors and the University will assume no responsibility if you violate this code. If you spill a chemical on your clothes, wash the affected area with tap water and notify the TA immediately to determine if some additional action should be taken.         
      • Be sure to note and follow any safety-related instructions within individual experiment descriptions.  Nearly all chemicals have some potential for harm, particularly if ingested, but most chemicals used in this laboratory do not represent an unusual risk.   You will be alerted to the danger and proper handling of any especially hazardous materials.  (Strong acids or bases, phenol, ethidium bromide and acrylamide are the main chemicals that you should exercise special care in handling.  Hot solutions should always be handled with care.)
      • Don’t clutter your work area with personal items such as backpacks, books, and clothing.  They often get in the way and end up on the receiving end of spills and splashes.
    1. Equipment.  Do not attempt to use any equipment until you have read and understood the operating instructions, or have been given appropriate instructions.  Treat all equipment with respect.  Don’t hesitate to ask the Instructor or TA if you have questions.
    2. Label the contents of all tubes, flasks, beakers, etc.  It is easy to forget or mix things up.  Marker pens and tape are available in the stockroom.
    3. Finish promptly.   We expect you to be on time for laboratory, to work continuously, and to finish by the end of the scheduled lab period.
    4. Clean up.  Wash all glassware and clean your work area prior to leaving.  Clean and return any borrowed equipment to its original location.
    5. Waste disposal. 
      • Do not put hazardous waste down the drain.  No organic liquids except ethanol should be put down the drain.  Water solutions are OK to pour down the drain unless you are told differently.   Waste containers will be provided for substances that require special disposal.  Check with the TA if you have any questions about disposal.
      • Do not put solid or powdered chemicals into ordinary waste cans.  There are marked containers for solid wastes. 
      • Do not put anything that is sharp or can be broken into ordinary waste cans.  All disposable glass and anything that is sharp should be placed in a specially marked ‘SHARPS BOX’    to prevent harm to the housekeeping staff.   Use the ordinary waste can only for paper and clearly harmless waste.   
      • In general, keep compatible wastes together.  That is, do not mix liquids with solids, organic liquids with water solutions, or acids with bases and the like.   

Contact with Instructor and TA's

Dr. Michael Blaber
406 Kasha Institute of Molecular Biophysics
(850) 644-1863
blaber@sb.fsu.edu

Hau Nguyen
244 DLC
644-7798
hau@sb.fsu.edu

Vedrana Marin
314 DRS 
644-2286 
vmarin@chem.fsu.edu

Office Hours

Monday 9:00 - 9:50 a.m., Room 406 Kasha Institute of Molecular Biophysics

Honor Code

Students are expected to uphold the Academic Honor Code. The Academic Honor System of The Florida State University is based on the premise that each student has the responsibility to:

1. Uphold the highest standards of academic integrity in the student's own work,
2. Refuse to tolerate violations of academic integrity in the University community, and
3. Foster a high sense of integrity and social responsibility on the part of the University community.

Click on Academic Honor Code for a full statement of the FSU Code.

While you may work with other students on the homework assignments, exams are an exercise in individuality. Any cheating on an exam will result in an automatic score of 0 points for that exam and may result in a grade of 'F' for the course.

ADA Requirements

This syllabus and other class materials are available in alternative format upon request.

Students with disabilities needing academic accommodations should:
1. Register with and provide documentation to the Student Disability Resource Center (SDRC).
2. Bring a letter to the instructor form the SDRC indicating you need academic accommodations. This should be done within the first week of class.


For more information about services available to FSU students with disabilities, contact the Assistant Dean of Students:
sdrc@admin.fsu.edu, Disabled Student Services, 08 Kellum Hall, Florida State University, Tallahassee, FL 32306-4066, (850) 644-9566.
 

Course Calendar

Date

 

Chapter

Subject

Text  pp

Lab report

Thu Jan 8

Lab

 

Check in

 

 

Tue Jan 13

Lecture 1

1

Basic practices and techniques, Laboratory notebooks, Presentation of data, Sections of a scientific report

1 - 49

 

Tue Jan 13

Lab

 

Safety and waste seminar

 

 

Thu Jan 15

Lab

 

Pipetting, techniques, accuracy and precision

 

YES

Tue Jan 20

Lecture 2

2

Spectrophotometry

53 - 69

 

Tue Jan 20

Lab

 

Measuring absorbance spectra, Spectroscopic determination of a pKa, A simple spectroscopic assay

 

YES
(Combined with lab below)

Thu Jan 22

Lab

 

Making buffers, buffering capacity

 

YES

Tue Jan 27

Lecture 3

3

Quantification of protein concentration

77 - 82

 

Tue Jan 27

Lab

 

Amino acid titration

 

YES

Thu Jan 29

Lab

 

Comparison of Biuret and Bradford protein assays

 

YES

Tue Feb 3

Lecture 4

4

Chromatography

89 - 116

 

Tue Feb 3

Lab

 

Separation of glucose-1-phosphate and glucose-6-phosphate by "normal phase" silica thin layer chromatography

 

YES

Thu Feb 5

Lab

 

Gel permeation and ion exchange chromatography on normal and CM-sephadex

 

YES

Tue Feb 10

Lecture 5

5

Gel electrophoresis of proteins

125 - 145

 

Tue Feb 10

Lab

 

Casting polyacrylamide gels

 

YES

Thu Feb 12

Lab

 

Analysis of blood proteins by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE)

 

YES

Tue Feb 17

Lecture 6

6

Overview of protein purification

157 - 173

 

Tue Feb 17

Lab

 

Non-denaturing PAGE.  Separation and identification of alkaline phosphatase

 

YES

Thu Feb 19

Lab

 

Ammonium sulfate precipitation practical (take home)

 

YES

Tue Feb 24

Lecture 7

7

Bacterial transformation (using pGLO)

 

 

Tue Feb 24

Lab

 

Isolation of GFP by chromatography

 

YES

Thu Feb 26

Lab

 

Electrophoresis of crude and purified GFP

 

YES

Tue Mar 2

Lecture 8

8

Enzyme kinetics

199 - 213

 

Tue Mar 2

Lab

 

Kinetics of wheat germ phosphatase, Progressive curves and range finding

 

YES

Thu Mar 4

Lab

 

Kinetics and product inhibition of wheat germ phosphatase, Vmax, Km and Ki

 

YES

Tue Mar 9

Spring Break

 

 

 

 

Tue Mar 9

Spring Break

 

 

 

 

Thu Mar 11

Spring Break

 

 

 

 

Tue Mar 16

Lecture 9

10

Ligand binding

247 - 271

 

Tue Mar 16

Lab

 

Equilibrium dialysis study of drug binding to DNA

 

YES

Thu Mar 18

 

 

 

 

 

Tue Mar 23

Lecture 10

11

Restriction mapping

277 - 299

 

Tue Mar 23

Lab

 

Electrophoresis of plasmid DNA

 

YES

Thu Mar 25

Lab

 

Isolation of plasmid DNA

 

YES

Tue Mar 30

Lecture 11

 

Recombinant DNA techniques (cont.)

 

 

Tue Mar 30

Lab

 

Restriction mapping of a plasmid

 

YES

Thu Apr 1

Lab

 

Transformation and growth of E. coli expressing green fluorescent protein

 

YES

Tue Apr 6

Lecture 12

12

Polymerase chain reaction (PCR)

313 - 323

 

Tue Apr 6

Lab

 

PCR LAB

 

YES

Thu Apr 8

 

 

 

 

 

Tue Apr 13

Lecture 13

13

Use of PC and internet for biochemical research

337 - 355

 

Tue Apr 13

Lab

 

INTERNET LAB ASSIGNMENT (combined with below)

 

YES

Thu Apr 15

Lab

 

INTERNET LAB ASSIGNMENT

 

YES

Tue Apr 20

Lecture 14

14

(Optional - the art and style of presenting scientific data)

N/A

 

Tue Apr 20

Lab

 

Instructor evaluation, Check out

 

 

Thu Apr 22

 

 

 

 

 

Tue Apr 27

Finals week

 

 

 

 

Tue Apr 27

Finals week

 

 

 

 

Thu Apr 29

Finals week

 

 

 

 

Last Updated on 12/29/03
By Dr. Michael Blaber

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