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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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