Course title

Biomedical Innovations I

Pre-requisite

Biology grade C or better both semesters: Chemistry grade C or better both semesters, (Chemistry can be concurrent or with instructors approval.

Course description

BioMedical Innovations I 2010-2011
Course Overview
This course is an overview of biomedical health technologies and the career possibilities in the biotechnology field. Students will be introduced to past; present and future applications of Biotechnology and learn proper lab procedures. Topics covered will include understanding laboratory procedures fundamental to biomedical research which include recombinant DNA; protein purification; cell and tissue culture. Additional topics include communication skills; the history and development of the field of biomedical research and understanding the legal environment and technology transfer aspects of biomedical research.

Emphasis is placed upon laboratory skills and data analysis. We will follow the CTE standards for Biomedical Health Technologies. Students will achieve an understanding of the major principles of biotechnology through their use of problem solving skills. Students will become proficient at collecting data and problem solving skills.

Course Expectations
A foundation of knowledge from introductory biology and chemistry is assumed so that most of our class time can be spent adding to and reinforcing your bank of knowledge rather than repeating what is already known.
Students are expected to complete reading assignments in the textbook prior to class. Topics will be presented/discussed then students need to clarify and reinforce concepts they did not completely comprehend from their textbook reading.

Laboratory Activities
Laboratory skills are an essential component to the course and will constitute more than 25% of the course. It is imperative that purpose and proper procedure are known before entering the laboratory. There will be pre- and post-laboratory discussions and write-ups to help solidify the concepts. Students will follow laboratory procedures properly as they use new equipment and learn new techniques necessary to be successful in the laboratory. Students will complete lab reports and will be evaluated on proper laboratory techniques.

Student Evaluation
A traditional grading scale (100-90 % = A; 89-80 % = B; 79-70 % = C; etc.) will be used for this course.

A test is given for each topic listed. The test will be modeled after the CTE standards and the Arizona state standards. Exams typically will have 35-50 multiple-choice questions and one essay question. Larger units may be divided into sections; with a test for each. The multiple choice questions are taken from the textbook as well as relevant questions from laboratory experiments. The essay question will be a performance based question that correlates with the concepts being tested. Reading quizzes and lab quizzes as well as skills tests will also be given throughout the course. Each semester grade is determined by the following:

Homework/Notebook 15%
(e.g.; completed study guides; activity worksheets;
problem sets; writing abstracts; article reviews)
Laboratory Work 35%
(including formal lab reports)
Exams and quizzes 50%
(Final exams are worth 15% of your semester grade)

Textbook:
Daugherty; Ellyn.. Biotechnology;. Paradigm Publishing Inc. 2007.
Student Lab Book:
Daugherty; Ellyn.. Biotechnology;. Paradigm Publishing Inc. 2007.
Proposed Course Outline Subject to Change Labs/Activities Chapters
I. Past; Present & Future Applications of Biotechnology (Daugherty)
A. Historical Applications of Biotechnology 1
Variety of Products
Scientific fields relating to biotechnology
Exploring Careers
Bioethics

Labs: Timeline-Evolution of Biotechnology
Replicate historical application of
biotechnology (e.g.; cheese; yogurt)
Field trips; guest speakers; web searches

B. Scientific Method & Lab Safety 1
Lab Safety
Setting up a Scientific Notebook
Problem solving using the Scientific Method
Graphing (Intro to Excel Graphing)
Biotech Skill Standards

Labs: Lab Safety Activities
Biotech Live- Biohazard (web search)
Lab Yeast Bioreactor (to model Sci Meth & Notebook with
Graph done on Excel)
Lab-Scientific Methodology in a Research Facility with Graphing with Excel & poster with logo)
Blue Jean lab
SOPs: Cleaning a Pipete; % error on balance & Pipete

II. Biochemistry

A. Cells 2
Prokaryotes vs Eukaryotes
Structure & Function of Organelles
Transport Across the Membrane
Levels of Organization
Cells Used in Biotechnology
Central Dogma of Biology
Macromolecules
Carbohydrates
Lipids
Proteins
Nucleic Acids
Plasmids

Labs:
Lab-Cell Study
Lab-Better Microscope Technique
Lab-Identifying Carbohydrates; Lipid & Proteins
Lab-Karyotype
Lab: Human Check Cell DNA Extraction (1 day)
Working Safely with Bacteria
DNA Extraction Exercise BioRad DNA in a Bottle)
Bioethics-Stop You Can?t Use Those Cells!

B. Basic Skills of the Biotechnology Workplace 3
Using a balance
Measurement with Metrics & Conversions
Measuring Mass & Volume
Compounds
Solutions
pH & Buffers
Hydrophobic/Hydrophilic
Molarity
Dilutions
Micropipetting

Labs:
Measurement Lab
Lab-Making Solutions
Lab-Using a Spectrophotometer to identify [MB]
Lab-Dilutions

C. Studying DNA 4.13
DNA Structure & Function
Sources of DNA
Prokaryotes and Plasmids
Eukaryotic DNA
Viral DNA
Isolating & Manipulating DNA
Using Gel Electrophoresis to Study DNA

Labs:

Lab-Making a DNA model
Lab-Bacterial Cultures
Lab-Gram Staining Bacteria
Lab: DNA Goes to the Races & Restriction Enzymes (1.5 days)(Carolina)
Lab-DNA Extraction from Bacteria
Lab-Gel Electrophoresis

D. Studying Proteins 5
Structure and Function of Proteins
Antibodies

Protein Synthesis
Mutations
Protein Catalysis
Applications of Protein Analysis
Biomanufacturing Proteins

Labs:

Lab-Making a Protein
Lab-Protein Separation and Identification
Through Chromatography w/ Ninhydrin
Lab-Blood Typing
Lab-Mutations
Lab-Enzymes
Lab-Rate of Reaction
Thinking Like a Biotechnician
Bioethics-Who Owns the Patent on the Genetic Code?

E. BIOINFORMATIC RESOURCES
Identify & Utilize electronic databases/websites (NCBI)
To search for relationships between protein
Sequences http://www.ncbi.nlm.nih.gov/

III. Biomanufacturing_______________________________

A. Identifying a Potential Biotechnology Product 6
Sources of Potential Products
The Use of Assays
Looking for New Products in Nature

Labs:

Biotech Online-Amazon Hide and Seek
Lab-How Do You Know You Have Amylase?
Lab-Assaying for Starch and Sugar
Activity-Assaying for Amylase
Lab-Isolating Horseradish Peroxidase from
Radish Root

B. Using a Spectrophotometer 7
Using a Spectrophotometer to Detect Molecules
Acids/Bases/Buffers
Using the Spectrophotometer to Measure Protein
Concentration

Using the Spectrophotometer in Medicine

Labs:
Lab-Learning to Use the Spectrophotometer
Lab-Calibrating and Using a pH Meter
Lab-Measuring the pH of Solutions
Lab-Determining the Concentration of Amylation
In Solution

C. Recombinant Biotechnology Product 8
An Overview of Genetic Engineering
Plasmid Technology
Polymerase Chain Reaction PCR
Transforming Cells
Making Recombinant DNA
After Transformation-Scale-Up
Fermentation

Labs:
Lab-Restriction Analysis with Lambda Phage
Transformation of E. coli with pAmylase
Lab-Growing & Monitoring Bacterial Cultures
Lab-Fermentation of Yeast (did one in IB 1st Q)

D. Bioethics
Cloning
Stem Cells
Eugenics
Gene Therapy
ELSI
Human Genome Project

Labs:
http://learn.genetics.utah.edu.
Web based exercise on Cloning
Web-Eugenic Movement

E. BIOINFORMATIC RESOURCES

Identify & Utilize electronic databases/websites (NCBI)
To search for relationships between protein
Sequences http://www.ncbi.nlm.nih.gov/

F. Biotechnology in Medicine 12
Drug Discovery

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IV Career Pathways in Biomedical Health Technologies
A. Survey the Biotechnology Field
Job Search Skills
Employability Skills
B. Develop Individual Career Plan
Prepare for Employment
Oral & Written Communication Skills
C. Quality Assurance
How to handle complaints; harassment; bioethics
D. Work-Based Learning

Labs/Activities:
Web-Search Activity & Presentation
Web-Search Laws and Restrictions
Write a Resume
Fill out Sample Applications
Write Cover Letter
Write a Letter of Recommendation
Mock Interviews

Final Project-Career Presentation
Prepare Pamphlet
Dress for Success

TYPICAL LAB
From Section II C Syllabus
Biotechnology Laboratory Manual: Ellyn Daugherty

Lab 4h?DNA Extraction from Bacteria

Background
Within bacteria cells; DNA and; therefore; genes are found both in the single genomic chromosome and in any extrachromosornal plasmids. Either source of DNA may be a source of genes for genetic engineering or gene therapy purposes.
Isolation of either type of DNA includes bursting open the cells; getting rid of contaminant
molecules; and precipitating the DNA out of the solution.
To burst open cells; the cell membrane must he removed. Since the major component of a membrane is a phospholipid bilayer; a detergent can be used to dissolve away this ?fatty? layer. Several different detergents may be used depending on the type of DNA to be extracted. For bacteria cells; SDS works well. Even household detergents; such as DawnÆ and IvoryÆ (both manufactured by Procter & Gamble); have been used.
When the cells burst; all the cellular contents are released into the collection vessel. The deter gent not only removes the lipids; but also precipitates many of the proteins from the membrane and cytoplasm. These proteins drop to the bottom of the vessel and are easy to separate from the DNA. Adding heat speeds the process.

Figure 4.14. Spooling Technique. When spooling; hold the glass rod almost parallel 10
the floor. Rotate and revolve through the two layers; scooping the DNA threads out and spinning them around the rod.

Enzymes may be added to degrade other molecules. For example; RNase is commonly used to decompose RNA contaminant molecules in DNA extractions. Proteases are used to degrade protein contaminants in samples.
Centrifugation can separate the precipitated proteins and degraded cellular debris from the DNA still in solution. The DNA can be drawn out of solution by adding alcohol; usually ethanol (EtOH).
or isopropanol. If chromosomal DNA is desired; the DNA can be spooled onto a glass rod (see Figure 4.14). Plasmid DNA is much too small to be spooled. It is precipitated from solution using a series of alcohol washes and centrifugation. Ultimately; plasmid DNA is recovered from one of the pellets left after one of the centrifugations. Plasmid isolation is presented in Chapter 8.

Purpose
Can relatively pure chromosomal DNA he extracted from E. coli bacteria cells?
Materials
E. coli broth cultures
(from Lab 4h)
Pipets; 10 mL
Pipet pump; green
Tubes; 15 mL capped
Tube racks for 15 mL tubes
Permanent lab marker pens
SDS; 10%
Water bath; 65∞C
RNase; 0.1 mg/mL
Protease; 0.1 mg/mL
5 M NaCI (from Lab 4a)
Centrifuge for 15 mL tubes
Beakers; 50 mL
Ethanol; 95%
Glass rods; 200 mm
TE buffer (from Lab 4a)
Pipets; 2 mL
Pipet pump; blue

Procedure
Safety Precautions
. Do all work in a sterile laminar flow hood or on a disinfected countertop.
. Use all standard precautions with the Bunsen burner; including tying back hair and wearing goggles; etc.
. Dispose of any bacteria-contaminated products in autoclave bags and/or 10% bleach solution.
1. Using sterile technique; add 10 mL of E. coli broth suspension to a 15-mL capped; conical; centrifuge tube.
2. Add 0.5 mL of 10% SDS to the tube with E. coli. Invert gently five times (5X) to mix.
3. incubate tube in a 65∞C water bath for 15 minutes.
4. Cool on ice for 5 minutes.
5. If desired; add 0.5 mL of RNase and 0.5 mL of protease to the tube. Invert
to mix.
6. Add 0.5 mL of 5 M NaCI. Place on ice for 5 minutes.
7. Spin the tube in a tabletop centrifuge
for 5 minutes (see Figure 4.15).
8. Gently decant or pipet the supernatant (top layer) to a clean; cold; 50-mL
beaker. Observe the color and viscosity of the solution. Create a data table
in your notebook to record these and other observations.
9. Place the beaker containing supernatant on ice for 5 minutes. W. Layer 5 mL of ice cold 95% ethanol slowly; with a pipet; down the inside of the beaker. Look at the interface
between the alcohol layer and the DNA layer. Do you see any evidence of DNA? Observe the color and viscosity of the solutions and interface. Record these observations into the data table.

11. 1-bld the beaker at a 45∞ angle and spool the bacterial DNA out of the solution. Slowly rotate a stirring rod clockwise; as well as up and down; and around; through the layers. Rotate and scoop at the interface instead of swirling. Every once in a while; pull up the rod and examine the DNA strands.
12. Try to spool all of the DNA strands. Observe and record the characteristics of the DNA
spooled sample in the data table.
13. Blot the eXCeSS FtOH off the sam- pie and place the DNA into a sterile; capped; conical centrifuge tube containing 2 mL of TE buffer. Immediately; observe and record the characteristics of the I)NA sample in the data table.
14. Allow the DNA to go hack into solution; over several days to a week; before using it for
further analysis. After a week; record the sampIes appearance in the data table. Store the
samples at 4∞C for 2 to 3 weeks. Long-term storage of the DNA samples should be at ?20∞C
(see Figure 4.16).
15. Test this sample for DNA; RNA contamination; and protein contamination using EtBr; DPA; and/or Biuret testing. Construct a clara table for the DNA; RNA. and protein data collection.
Figure 4.16. DNA; RNA; and most proteins are temperature-
sensitive and may be degraded or denatured by enzyme
contaminants (eg; proteases or DNases) at room temperature. To
decrease their activity and preserve molecular or cellular
samples; most are stored at ?20∞C or ?80∞C. This ?80∞C freezer
stores DNA samples for sequencing.
Photo by author.

Data Analysis/Conclusion
Describe the quality and quantity of DNA extracted from the bacterial cell sample compared with other DNA samples you have spooled. Discuss how effective the DNA extraction technique is at isolating pure DNA. Give evidence for your statements. Propose variations in the protocol that may lead to improved quantity or purity of the DNA sample.

Thinking Like a Biotechnician
1. Protease is used in this experiment to chop UI) protein contaminants. There are many
different kinds of proteases. One protease that can be purchased at the grocery store is
papain. a protease derived from papayas; which is found in meat tenderizers; such as
AdolphsÆ meat tenderizer (by Lawry?s). How can one know that 1 mg/ml. of papain is the
best concentration of the proease to use? Describe a simple experiment to determine the
best concentration for protease activity.
2. You used 10% SDS in the experiment Lo explode the bacteria cells and precipitate protein
contaminants. One can purchase 2?Yo SDS commercially. How much 20% SDS would you
need to have enough to make 2000 mL of 10% SDS? .
3. The genomic DNA that was spooled was considerably less in volume than the salmon
sperm DNA spooled in a previous lab experiment. What is the reason for the difference in
DNA yield? .

School Country

United States

School state

Arizona

School city

Scottsdale

School Address

8500 E. Jackrabbit Road

School zip code

85250

Requested competency code

Lab Science

Date submitted

11/1/2010

Approved

Yes

Approved competency code

• CTE
• Career and technical education

• LADV
• Advanced science

• LBIO
• Biology

Approved date

11/1/2010

Online / Virtual

No