TEMPLATE
Biotech I
Queen Creek High School
2018 –19 Course Syllabus
Course: Biotechnology I
Instructor: Mr. Popham
Phone: (480)987-5973 ext. 4640
Email: jpopham@
Room: B120
I will be available in my other classroom B138 before and after school if you have any questions.
Course Description:
This course is an overview of biotechnologies 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 bioscience. 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.
Textbooks used: Biotechnology: Science for the New Millennium by Ellyn Daugherty
For a full list of ADE State standards go to: (Biosciences)
Course Materials:
Students are expected to bring the following to class each day:
▪ Pens in black or blue ink
▪ Pens in red ink pens
▪ Three ring binder to keep handouts and your daily work in
▪ Composition book for your Lab notebook
We are proud to support AVID strategies throughout our school. In our class, students will use numerous organization strategies, graphic organizers and WICOR strategies. We encourage all students to develop a plan for after high school. We will encourage all students to explore college and career options.
Binders: All 9th and 10th grade students are expected to keep a clean, organized binder throughout the year. All 9th and 10th grade binders must include:
· Tabbed Dividers that can be labeled for each class (6 total)
· A pencil pouch with pencils, pens, highlighters, colored pencils, and a ruler
· Notebook paper or Cornell Note paper.
Planners: All 9th and 10th grade students will be provided with an agenda planner/daily calendar to help them record assignments for all of their classes plus extracurricular activities, chores and other home responsibilities. Planners will be checked weekly and Incentives will be provided to students who use their planner to help keep themselves organized.
HOSA-(Future Health Professionals)
HOSA is the state and national student career and technical student organization that is co-curricular. Students will have opportunities to participate in various projects in class and possibly compete at local competitions. Information of HOSA events will be sent home periodically throughout the school year. Participation in HOSA provides a student with many opportunities for scholarship at the local, state, and national level. We also follow the No Pass/No Play guidelines.
Lab Expectations
• Use tools and lab equipment as instructed
• Wear proper PPE while working at a lab station.
• Put all tools/lab equipment and parts back in their respective places/containers when done
• Ensure work space is clean and neat before leaving class
Grading System:
100 – 98 |= |A+ |83 – 80 |= |B- |66 – 64 |= |D | |97 – 94 |= |A |79 – 77 |= |C+ |63 – 60 |= |D- | |93 – 90 |= |A- |76 – 74 |= |C |59 – 0 |= |F | |89 – 87 |= |B+ |73 – 70 |= |C- | | | | |86 – 84 |= |B |69 – 67 |= |D+ | | | | |
Late Work Policy: Per the student handbook, late work will be accepted until the end of each unit for a maximum of 50% credit (this includes unexcused absences). Excused absences will have one day for each absence to make up.
Extra help: It is the student’s responsibility to make arrangements with Mr. Popham for any extra assistance before or after school.
Daily Bell Work: Each day, there will be bell work assignment written on the board. Students are expected to be working on this assignment each day when the bell rings and keep the ‘bell work sheet’ in their binder to be turned in and checked.
Group Projects: This class consists of many projects, some of which will be group projects. Take responsibility for your portion of group assignments, be present with your materials on the due date or make sure your materials are sent to school if an absence is unavoidable. Failure to do so will result in loss of points as determined by Mr. Popham.
Classroom Management Plan:
Student Behavioral Expectations:
1. Be on time and prepared.
2. Respect people and property.
3. Follow directions.
4. Keep your hands, feet, and other objects to yourself.
5. Follow all school rules.
Consequences – If you choose to ignore an expectation:
First time: Verbal warning/Conference
Second time: Notification of Parent/Guardian
Third time: Detention/Conference/Meeting with Parent/Guardian
Fourth time: Written referral
Severe offense: Immediate removal by security
(Severe offenses include: alcohol/drugs, fighting, threats, verbal abuse, intimidation, hazing, etc.)
Rewards – Following the rules will bring you:
• Daily praise
• Positive notes/calls home
• Success in this class and the outside world!
Cheating/Academic Misconduct: There is zero tolerance policy for cheating in this class. Students involved in cheating (including the student who is letting someone cheat from him/her) will receive an automatic zero on the assignment and a phone call home will be made to the parent/guardian. A second offense will result in a referral and appropriate disciplinary action.
Cellphones and Electronic Devices: Students are permitted to use cell phones and other electronic devices during instructional time with teacher permission. Students must turn in their cell phone when going to the bathroom or other non-instructional areas. If a student has a phone in the hallway during instructional time, it will be confiscated by campus administration and returned upon conclusion of the school day.
Drinks on Campus: Drinks with a twist off cap only will be permitted on campus. This is a lab so only water is allowed.
Food Deliveries: Outside food delivered to the front office may only be picked up during lunch or passing periods in order to honor instructional time.
Skateboards: Skateboards must be dropped at the administration office in order to avoid damage or theft. Skateboards can be picked up after 2:00 in the administration office.
Wireless Speakers: Music played from wireless speakers is not permitted during school hours.
Restroom Use: The restroom should be used during the breaks. The restrooms cannot be used the first 10 minutes and the last 10 minutes of class. You must put your cellphone in the lock box and take the pass. If you are found in the hall with a cellphone during instruction time it will be confiscated and returned at the end of the day.
Absences: It is the student’s responsibility to pick up any work missed. It is very important that your child is in class every day. All school and district attendance policies will be upheld. Excessive absences will limit a students’ success.
Return this portion to Mr. Popham
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Dear Parent or Guardian;
I want to take this opportunity to introduce myself and express my excitement about working with you and your son/daughter this year. Your student is enrolled in Biotechnology I class at QCHS which is part of the HOSA program. As part of the program in this area, your student will have the opportunity to work with many pieces of lab equipment. Each student will be directed in the proper use of the equipment and safety instructions will be given. The student needs to take responsibility for his/her individual actions in regards to safety.
Parents, also note that your student will be watching the movies Gattaca and The Martian part of our discussion on biotechnology and ethics. By signing below, you agree that they will be allowed to watch these films. If not, an alternate assignment will be given.
To show your understanding of these rules, please sign the following permission slip (multiple areas to sign). Students will be able to participate in the lab only AFTER they have returned this letter completed.
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I give my permission for __________________________________ to use equipment in biotechnology I class when supervised by a qualified instructor.
Parent/Guardian Signature: ____________________________________________Date:_____________
I give permission for my student to view the films Gattaca and The Martian
Parent/Guardian Signature: ____________________________________________Date:_____________
I have read the above statements and understand that I am responsible for my actions.
Student name printed: ______________________________________________Period: _____________
Student signature: __________________________________________________Date:________________
I understand and will adhere to the No Pass, No Play policy and will work to the best of my ability to maintain a C average in all of my classes.
Student name printed: ______________________________________________Period: _____________
Student signature: __________________________________________________Date:________________
My goal is to ensure that all students will be successful in this course and motivated to do the best they can. Your help in this endeavor is greatly appreciated.
I am excited about working with your student and am looking forward to a great year!
Sincerely, Mr. Joshua Popham
Biotech Course Outline
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
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
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:
.
Web based exercise on Cloning
Web-Eugenic Movement
E. BIOINFORMATIC RESOURCES
Identify & Utilize electronic databases/websites (NCBI)
To search for relationships between protein
Sequences
F. Biotechnology in Medicine
12
Drug Discovery
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 Dawn® and Ivory® (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
Adolphs® 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 2ŒYo 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? .
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I am a believer that everything we do is worth value so therefore every assignment is of approximate equal value. With each term being 9 weeks each week equals approximately 5% of your grade, and the final is 20%.
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