michelle landreville biotechnology unit 1: the lab ... · pdf filemichelle landreville...

NAU BIOTECH Unit 1 of 12: BIOTECHNOLOGY: Lab Techniques & Data Analysis of 21

NAU BIOTECH © 2009 Michelle Landreville

Michelle Landreville Biotechnology Unit 1: The lab techniques and analysis of the data Introduction to Biotechnology Unit: Students will demonstrate knowledge of biotechnology concepts and apply knowledge to real-world problems in inquiry-based laboratories. Emphasis will be on lab technique and analysis of the data. (Each lesson in this unit teaches concepts that will be used for prior knowledge in the next lesson. Please see general concepts of each lesson to view the continuing concepts of this unit.) All Arizona standards are for high school unless indicated. Research for this unit includes information from Recombinant DNA and Biotechnology: A Guide for Teachers (Recombinant DNA), 2001. The National Science Education Standards (NSES), 1999; Making Sense of Secondary Science: research into children’s ideas (Making Sense), 1994; Benchmarks for Science Literacy (Benchmarks), 1993. Preceding Units: The unit preceding the biotechnology unit would include mitosis / cell reproduction, a comprehensive unit on DNA and protein synthesis. Much of the prior knowledge needed to link and understand concepts would be taught in these preceding units. General Concepts for Biotechnology Unit (NSES) Scientific Literacy NSES p.22“Scientific Literacy is the knowledge and understanding of scientific concepts and processes required for personal decision making, participation in civic and cultural affairs, and economic productivity.” Knowledge and Understanding NSES p. 23“Scientific knowledge refers to facts, concepts, principles, laws, theories, and models and can be acquired in many ways. Understanding encompasses the ability to use knowledge and…distinguish between what is and what is not a scientific idea.” Inquiry NSES p.23“Inquiry refers to the activities of students in which they develop knowledge and an understanding of scientific ideas, as well as an appreciation of how scientists study the natural world. Inquiry is a multifaceted activity that involves making observations; posing questions; examining (other sources) to see what is already known; planning investigations; …using tools to gather, analyze, and interpret data; proposing answers, explanations and predictions; and communicating results.” Students should engage in multiple levels of investigation including the ability to develop and conduct inquiry investigations. Science and Technology NSES p.24“The goal of science is to understand the natural world and the goal of technology is to make modifications in the world to meet human needs. The need to answer questions in the natural world drives the development of technological products and they in turn provide the tools that promote the understanding of natural phenomena.” Time Frame: seven 50 minute class periods Unit Outline: Lesson 1: DNA Extraction (2 50 min periods) Lesson 2: Paper recombinant plasmid (1 50 min period) Lesson 3: pGLO lab (2 50 min periods) Lesson 4: Dye Electrophoresis (1 50 min period) Lesson 5: DNA Fingerprint Lab (1 50 min period) Lesson 6: T-Gen Lab: “DNA Chips: From Genes to Disease”(1 50 min period)

http://www.nap.edu/openbook.php?record_id=4962&page=22






Day 1 & 2 “DNA Extraction” Time Planned for activities: two class periods (50 minutes each) Prior Knowledge Needed:

Structural formula and function of DNA within organisms. Difference between plant and animal cellular structure. Basic measurement skills for measuring liquid volumes from 5mL–25 mL.

General Concepts: DNA is a universal element that exists in all life forms. While all DNA has the same chemical structure and therefore looks the same, it is the sequence of nucleotides that distinguishes not only one organism from another but one individual from another. DNA extraction is the basic process for all DNA testing. Standards: NSES Content Standard C: Life Science grades 9-12; The Cell. NSES p. 184 “Cells have particular structures that underlie their functions. Every cell is surrounded by a membrane that separates it from the outside world.” The Molecular Basis of Heredity. NSES p.185 “In all organisms, the instructions for specifying the characteristics of the organism are carried in DNA, a large polymer formed from subunits of four kinds. AZ State Standards Science Standards

Strand 1: Concept 1: PO3 Concept 2: PO2

Strand 4: Concept 1: PO2 Student Misconceptions: “Students have difficulty thinking about the human body as a chemical system and have little knowledge about the elements composing the body.” (Benchmarks p. 342) “High school and college students mainly use obvious criteria to distinguish between living and non-living and rarely mention structural criteria or biochemical characteristics (DNA).” (Benchmarks p. 341) Essential question: What does DNA look like? Can DNA be extracted? Can the individual bases be seen? What methods must be used for DNA to be extracted? Day 1 behavioral objectives:

Students will demonstrate correct technique for successful extraction of DNA from strawberry and / or kiwi (or alternate source).

Students will justify the use of reagents for DNA extraction. Description: Students know the structural basics of DNA from previous units, but what does it actually look like? Can you see the A,T,G, and C ‘s? Does all DNA look the same? Students will use one or two types of fruit to practice DNA extraction and further their studies on Day 2 by extracting DNA from plant, animal, or even bacterial samples. Common everyday items such as tap water, liquid dish detergent, salt, coffee filters, and meat tenderizer will be utilized. This is a simple lab to perform at low cost. (The fruit is the costliest part of the lab.) Time needed is one 50-minute class period. (Anderson, N. (2002). The



http://azed.gov/standards/science/highschool.pdf



University of Arizona Biotech Project: Mobile biotechnology for the classroom, from http://biotech.biology.arizona.edu/labs/labs.html) Inquiry Level: Level 2 inquiry. Students should form testable questions. The procedure is provided by teacher and discussions will be led by teacher. The teacher will also provide materials (overheads of cell models, etc) to induce students’ prior knowledge of cellular structure. Students should formulate responses as to why each reagent was used and why it is relevant in the DNA extraction procedure. Students will answer teacher-made worksheet questions to help organize ideas into development of procedures for day 2 extraction lab, i.e. how is extraction different between animal and plant cells? Materials Needed & Hints: (see appendix for worksheets) Many lab companies produce ready-made kits for DNA extraction (BioRad- Genes in a bottle). A simple, inexpensive kit can be assembled, stored, and used each year. See Teacher DNA Extraction Lab Instructions and student worksheet. Purchase perishable items the day before the lab. Large samples of fruit can be cut into 2 or 3 pieces. Use freezer bags to prevent rupture during the lab. Wire mesh coffee machine filters are much faster than paper filters. Students need lab notebook.

Safety Concerns: None*. Inert chemicals are used. Clean up is with soap and water. As with all labs, students must wash hands before leaving the lab area. *Goggles are needed if allowing students to add the ethanol to test tubes. Ethanol should be washed from skin with soap and water. Ethanol in the eye should be continually flushed with water for a minimum of 15 minutes using eyewash.

Assessment: 1. Observable DNA. Did students follow the procedures to produce visible quantities of DNA? (Samples of DNA may be placed in microtubes with ethanol and taken home.) 2. Students will answer questions from teacher-made worksheet (individual or group). Worksheet and description of DNA will be glued into lab notebook. Worksheet will be graded for points from teacher-made rubric. Application / Real-World Connection: Once DNA has been extracted, it can then be purified from other cellular “debris” and used for sequencing, DNA fingerprinting, genetic analysis, PCR, and other experiments. Extraction is the first step of all other DNA-based experiments. Day 2 DNA Extraction Prior knowledge:

Students must use and understand technique learned in day 1 extraction. Students must modify procedures for today’s lab according to the type of organism used for

extraction (plant vs. animal). If students understand the concept of DNA being universal, they should be able to predict an

outcome for today’s extraction. “Important (to inquiry) is the prior establishment of an adequate knowledge base to support the investigation and help develop scientific explanations.” NSES p.174 General Concepts: DNA is a universal element that exists in all life forms. While all DNA has the same chemical structure and therefore looks the same, it is the sequence of nucleotides that distinguishes not only one organism from another but one individual from another. DNA extraction is the basic process for all DNA testing.

http://biotech.biology.arizona.edu/labs/labs.html




Standards: NSES Content Standard A: Science as Inquiry grades 9-12; Developing Student Abilities and Understanding. “A critical component of successful scientific inquiry in grades 9-12 includes having students reflect on the concepts that guide the inquiry.” NSES p.174 Content Standard C: Life Science grades 9-12; The Cell. “Cells have particular structures that underlie their functions. Every cell is surrounded by a membrane (plasma and nucleic) that separates it from the outside world.” NSES p.184 The Molecular Basis of Heredity. “In all organisms, the instructions for specifying the characteristics of the organism are carried in DNA, a large polymer formed from subunits of four kinds.” NSES p.185 Matter, Energy, and Organization. “The complexity and organization of organisms accommodates the need for obtaining, transforming, transporting, releasing, and eliminating the matter and energy used to sustain the organism.” NSES p.186 AZ State Standards Also see Day 1 extraction performance objectives. Science Standards

Strand 1: Concept 1: PO4 Strand 4: Concept 2: PO1 Concept 5: PO2

Misconceptions: See Day 1 extraction objectives Essential questions: Does DNA from different organisms look different? Do different sources produce different amounts of DNA? How must the extraction protocol be modified for different organisms? Day 2 behavioral objective:

Students will extract and compare DNA from a variety of sources. Students will modify lab procedures to each specific organism as necessary. Students will justify the modifications to the procedures.

Description: See day 1 extraction. Students will be able to answer the essential questions and (hopefully) draw the conclusion that DNA will appear the same because all DNA is derived from the same code. Time needed is one 50-minute period. Inquiry Level: Inquiry level is 2+. Teacher initiates question: Does all DNA look the same? For lower-level inquiry, teacher may provide procedures for various organisms. For higher-level inquiry, students must determine a set of procedures for each organism. Materials: A variety of organisms to test. Suggestions are given in teacher guide (see appendix). Materials will vary depending on what teacher or students select to test. Supplies remain the same. May need a mortar and pestle to grind samples. Teacher prepared overhead for each student group to add data to be shared by the class.

Safety Concerns: *If using bacteria, prepare a 10% bleach solution for any equipment that comes in contact with the bacteria. See day 1 for general safety and clean up.








Assessment: Students will complete a reflection including written and drawn components. Students will draw metaphoric representation of extraction. Written component should include basic procedures describing the drawings and a summary comparing the DNA extraction process from at least 3 different organisms and any modifications they made to the procedure and why. Assessment can be completed individually or divided into group components. Students will provide data on teacher-made overhead. All organisms tested will be included and copied into student notebooks. Students will provide a written one-paragraph summary of the Day 2 essential questions using data from this lab. Drawings with description and summaries will be graded according to a teacher-made rubric. Application / Real-World Connection: Once DNA has been extracted, it can then be purified from other cellular “debris” and used for sequencing, DNA fingerprinting, genetic analysis, PCR, and other experiments. Extraction is the first step of all other DNA-based experiments. Extraction procedures often have to be modified depending on the type of organism extracted from and whether the DNA is genomic or plasmid. Day 3 “Paper recombinant plasmid” Time Planned for activities: One 50-minute period. Prior Knowledge:

Structure of DNA molecules and knowledge of complimentary base pairing. Recall what a palindrome is by asking students for examples learned in language arts classes and

apply this to DNA for use with restriction enzymes. General Concepts: “The restriction enzymes commonly used in laboratories generally recognize specific DNA sequences of 4 or 6 bases… and are palindromic.” (Massey, p. 190). Recombinant DNA technology is used to create genetically engineered organisms. Restriction enzymes can be used to cut DNA fragments from different organisms and various enzymes can be used to splice the sections back together. Standards: NSES Content Standard G History & Nature of Science; Historical Perspectives “Usually, changes in science occur as small modifications in extant knowledge.” NSES p.201 Content Standard C: Life Science grades 9-12; The Molecular Basis of Heredity. “In all organisms, the instructions for specifying the characteristics of the organism are carried in DNA, a large polymer formed from subunits of four kinds.” NSES p.185 Matter, Energy, and Organization. “The complexity and organization of organisms accommodates the need for obtaining, transforming, transporting, releasing, and eliminating the matter and energy used to sustain the organism.” NSES p.186 AZ State Standards: Science Standards Strand 2: Concept 1: PO3 Strand 4: Concept 2: PO1 Concept 5: PO2







Misconceptions: “…pupils thought bacteria could be useful when dead, for making medicines or vaccines, but there was little evidence of notions about the technological potential for living microbes.” (Driver, et al. p.57) Essential Question: How is recombinant DNA created? What is a plasmid? What is the source for plasmids? What is recombinant DNA? Behavioral Objective:

Students will create a paper model of a recombinant plasmid using (scissor) restriction enzymes. Students will identify the sequence of target bases for each DNA strand.

Description: (Use 2 different colored papers) *See Biology: The Dynamics of Life textbook p.p. 380-381 for instructions. The teacher may pre-copy the DNA sequences onto paper, photocopy onto colored paper, and cut the paper into the prescribed strips. This will help the students focus on the recombinant technique and not be confused by the procedure. It is important for students to have a conceptual understanding of the process and impact of recombinant DNA, especially in relation to the pGLO lab. Inquiry Level: Level 1. Much of this activity is either teacher directed or uses the procedures outlined in the text. Materials: scissors labeled “restriction enzymes”, 2 different colors of copy paper, transparent tape or stapler, textbook or copied instructions.

Safety: scissor safety

Assessment: Students will attach the paper plasmid and answer analysis questions from p. 381 of text (Biology: The Dynamics of Life) in their lab notebook. Teacher may also ask students for an oral summary of what was learned and how this technology can be applied in the real world. Application / Real-World Connections: Recombinant DNA has many applications in agriculture, industry and medicine. Students may research such as the production of insulin, human growth hormone, and vaccines. Extensions could also be explored in regard to genetic engineering in legal, social, and ethical aspects. Students will use a recombinant plasmid in the pGLO lab. Day 4 & 5 “pGLO lab” Time needed to complete activity: two 50-minute period. Prior Knowledge:

Structure of DNA. Technique of creating recombinant DNA. The uses of restriction enzymes are important concepts for students to have in order to fully

understand the implications of the pGLO lab. General Concepts: Genetic transformation requires specific steps and sterile techniques are important to practice when working in lab setting. Operons activate genes to produce protein products. Genetic engineering can be applied to all aspects of human health, farming, manufacturing of pharmaceuticals, and research..



1. Students will be able to describe the necessary steps involved in genetic transformations and how scientists select for transformed (transgenic) organisms.

Students will be introduced to how operons activate genes in order to produce protein products, with an emphasis on the arabinose operon.

2. Students will be able to apply the concept of genetic engineering to other aspects of human health and treatment.

Students must follow a strict protocol in order for this lab to be successful. Sterile techniques in the laboratory will be practiced.

3. Students will practice sterile techniques in the laboratory.

*THE NUMBERED ITEMS ARE STUDENT OBJECTIVES. Standards: NSES Content Standard A: Science as Inquiry grades 9-12; Developing Student Abilities and Understanding. “Conceptual principles and knowledge guide scientific inquiries.” NSES p.176 Content Standard E: Science and Technology; Understandings About Science and Technology. “Science often advances with the introduction of new technology.” NSES p.192 Content Standard F: Science in Personal and Social Perspectives; Science and Technology in Local, National, and Global Challenges. “Progress in science and technology can be affected by social issues and challenges.” NSES p.199 Historical Perspectives “Usually, changes in science occur as small modifications in extant knowledge.” NSES p.201 AZ State Standards: Science Standards

Strand 1: Concept 2 Strand 2: Concept 1: PO3

Misconceptions: “Prior beliefs were found to be the major influence in a pupil’s understanding of the experiments…that use sterile control plates in a bacteriological experiment (and) could not be understood if a child’s concepts of living, size, growth, and reproduction in bacteria are not understood.” (Driver et al., p. 57) “Students have difficulties understanding that changing a population results from the survival of a few individuals that reproduce, not from the gradual change of all individuals in the population.” (Benchmarks p. 343) “Students did not recognize the possibility of bacterial contamination on unsterilized equipment. (Bacteria) were not identified as living organisms because they were not visible nor causing disease. Students could describe (bacterial) colonies and say that a colony consisted of many individuals, but could not explain size differences. (Driver et al. p. 58) Tracing historical treatments and connecting increased benefits with technology is also applicable. “High school students may have difficulties understanding the views of historical figures. Students may think of historical figures as inferior because they did not understand what we do today.” NSES p.200 Essential Question: Why is sterile technique important? What is the outcome if sterile technique is not followed? How is sterile technique performed?









Day 4 Behavioral objective: (Pre-lab)

Students will demonstrate proper use of lab equipment (i.e. fixed pipettes, plating, and streaking technique).

Students will practice using sterile technique. Description: Students will be introduced to a bacterial transformation lab which is essentially the same process used in research and commercial labs to produce new drug therapies and protein products. The first day is a pre-lab day where students can practice the techniques of streaking an agar plate without gouging the surface and alliquoting liquids smaller than 1 mL with a fixed pipette. Sterile technique will also be demonstrated and practiced. Time required is two full class periods; one for practice and one for transformation. Inquiry Level: Level 0. This pre-lab instruction is teacher led to demonstrate and allow students to practice with the lab equipment and refine techniques needed for a successful transformation lab. Materials: one set of equipment for each lab group of students: Large agar plate Bacterial loops (non-sterile ok) Fixed pipette and overhead of pipette measurements Micro test tube 50 mL beaker with 10mL water

Safety: No safety precautions with this lab. Teacher will introduce sterile technique, but no bacteria will be used.

Assessment: Each lab group (3-4 students) will be given a lab skills protocol checklist. Students must record and check that each skill was successfully accomplished. Teacher may also desire to sign off on student skills. Application / Real-World Connection: Sterile technique is extremely important when working with bacteria and DNA in general. Contamination can result in failed experiments or mutations from foreign DNA or microbial contaminants. Students will use techniques learned today and apply them to the pGLO bacterial transformation lab. Essential Questions: How is bacteria used to produce substances (proteins) from other organisms? How can plasmids be inserted into another bacterium? Why is this technology important? What applications can be derived from bacterial transformation? Day 5 Behavioral objective:

Students will perform bacterial transformation lab and lab analysis. Description: Students will perform the pGLO transformation lab. There is a strict procedure that must be followed in order to have successful transformation and bacterial growth. Students may need to observe bacterial growth and complete analysis on the following day. One full class period (minimum 50 minutes with NO spare time) is required. BioRad pGLO Transformation Kit



Inquiry Level: Level 2. The protocol must be strictly followed; however, the evidence, explanation, and real-world connections are student generated. Teacher may need to facilitate a discussion. For example, students may have a difficult time connecting why the +plasmid bacteria grows on the LB/amp plate, but does not glow green. (This plate does not contain arabinose.) Materials: Bio Rad pGLO transformation kit. ***This kit contains enough supplies for 2 classes of 32 students each. Additional equipment not included is listed below. Incubator (37 ° C) Hot water bath (42° C) Using DI water will prevent mineral deposits. 2-4 U-V/ black lights (green fluorescent protein cannot be observed without this light) Ice and small Styrofoam cups Sharpie markers or wax pencils – 1 per group Masking tape Buckets or other containers with 10% bleach solution **The preparation time for this lab can be up to 2 hours the first time. Experienced teachers with this lab can complete set up in about 1 hour. Bacterial cultures need to be started 24 hours before the lab and should be no older than 36 hours. LB and other plates can be made up to 1 week before the lab and stored in the refrigerator. Instead of disposing of equipment after bleaching, many items can be washed in hot, soapy water and used for other labs throughout the year. Autoclaving is another option.

Safety: The E. coli used in this lab in non-pathogenic, but should be treated as such in the lab. All participants should wear goggles and gloves. All lab supplies, except paper products, should be placed in a 10% bleach solution and soaked overnight. Teacher can then place items in a double plastic bag and place in the trash. DO NOT DISPOSE OF AGAR DOWN THE

DRAIN. It will solidify and clog the drain. Equipment can also be autoclaved before disposal. Assessment: REE, PE, PA in student lab notebook graded with teacher-made rubric. Emphasis should be placed on the evaluation of the results and the applications. REE = Results with evidence and evaluation, including drawing and description of bacterial cultures. PE = Possible errors. PA = Practical applications of this lab or technology Application / Real-World Connection: Many drugs are currently being produced with biotechnology. Most students know someone with diabetes or cancer. Through this lab, students are introduced to technology and how drug companies use bacteria and other organisms to make human proteins for treatment of these diseases and others, i.e. if a gene product is produced, it can be purified and used. Day 6 “Dye Electrophoresis” Time Planned for activities: one 50 minute class period Prior Knowledge:

Knowledge of DNA structure and how to extract DNA from an organism. Application of restriction enzymes. Introduction to using and measuring with micropipettors, making agarose gels, and loading samples

into wells. Much practice is gained during this lab.



General Concepts: DNA has an overall ionic charge (-). An electrical current can be used to separate DNA by size in an agarose gel. Larger DNA fragments cannot travel as far as smaller ones. DNA fragments of the same size will be located in the same area of their respective lanes. Standards: NSES Content Standard A: Science as Inquiry Developing Student Abilities and Understanding “Conceptual principles and knowledge guide scientific inquiries.” NSES p.176 Content Standard B: Physical Science; Motions & Forces “Opposite charges attract while like charges repel.” NSES p. 180 Content Standard G: History and Nature of Science; Science as a Human Endeavor “Individuals and teams have contributed and will continue to contribute to the scientific enterprise.” NSES p.200 AZ State Standards: Science Standards

Strand 1: Concept 2: PO4 Strand 2: Concept 1

Misconceptions: “Students can understand and use the engineering model-that is, students think about producing desirable outcomes before they are able to do more analytic form of thinking involved in scientific inquiry. Students appear to understand the impact of science on technology, but they do not always appreciate the impact of technology on science.” (Benchmarks p. 334) Essential Question: How can DNA be used for comparison? How is electricity used to separate DNA fragments? How are DNA gels prepared? What is gel electrophoresis? Behavioral Objectives:

Students will demonstrate correct technique for making, pouring, and loading gels. Students will analyze “DNA” banding on gels.

Description: Students are able to practice lab skills necessary to experiment with DNA while using dyes, which are relatively inexpensive materials. This simple lab is a very good indicator of lab skills before students experiment with costlier DNA and restriction enzymes. The teacher may save time by pre-pouring gels and distributing to students. Inquiry Level: Level 2. Students are given a procedure, but skill level and interpretation of the results is student oriented.








Materials: From BIOTECH Project, U of A 4-5 chemical dyes and unknown dye (2 or more dyes in same tube) microtubes P-20 micropipettors and tips Gel boxes and power source 0.8% agarose in 1X TAE (prepared and in hot water bath to keep liquefied) 1X TAE buffer clear plastic rulers overhead sheets colored pencils or permanent markers laboratory tape

Safety: Power source should be unplugged until samples are loaded and ready to run. Always make sure hands are dry and spilled liquids are cleaned up before using electrical equipment.

Assessment: Students will measure the banding patterns and record them, using colored pencils, in their lab notebooks. Another alternative is to trace the bands onto overhead sheets, cut out, and attach in the lab notebook. Students will answer teacher-made worksheet questions that probe comprehension of the lab and explore possible errors. Application / Real-World Connection: Students can learn the basic procedures of loading, running, and analyzing gels and apply this knowledge to the DNA fingerprint lab. Other applications will be discussed in the Day 7 lab. Day 7 “DNA Fingerprint Lab” Time Planned for activities: one 50 minute class period Prior Knowledge:

Knowledge of DNA structure and how to extract DNA from an organism. Application of restriction enzymes. Lab experience using and measuring with micropipettors, making agarose gels, and loading samples

into wells. Analysis of DNA banding patterns.

General Concepts: Restriction enzymes have a multitude of purposes. Restriction enzymes cut double-stranded or single stranded DNA at specific restriction sites. The resulting fragments can be used for gene mapping. It allows researchers to compare DNA samples from different sources. Linear base pair sequences will be cut by the same restriction enzymes. If two or more samples of DNA are cut using the same enzymes, they can be analyzed using DNA fingerprinting methods. DNA fragments of the same size will migrate and stay together in the same bands respectively. DNA can then be analyzed for similar banding patterns. This can indicate a relationship between DNA samples. “The bottom line on inherited differences is in DNA. As a result of biotechnology, we can now look directly at DNA to study differences is various populations, to screen for disease, to screen for paternity, and to identify individuals.” (Kreuzer and Massey, p. 267)



Standards: NSES Content Standard A: Science as Inquiry Developing abilities and Understandings of Inquiry “Conceptual principles and knowledge guide scientific inquiries.” “Scientific explanations must adhere to criteria such as: a proposed explanation must be logically consistent; it must abide by the rules of evidence, it must be open to questions and possible modification; and it must be based on historical and current scientific knowledge.” NSES p.176 Content Standard C: Life Science; The Molecular Basis of Heredity. “Changes in DNA (mutations) occur spontaneously at low rates. Some of these changes make no difference to the organism, whereas others can change cells and organisms. Only mutations in germ cells can create the variation that changes an organism’s offspring.” NSES p.185 Content Standard G: History and Nature of Science; Historical Perspectives “Usually, changes in science occur as small modifications in extant knowledge.” NSES p.201 AZ State Standards: Science Standards

Strand 1: Concept 1: PO1 Concept 2: PO1 & PO4

Strand 2: Concept 1: PO3 Strand 4: Concept 2: PO6

Misconceptions: “Students have some understanding that characteristics are determined by a particular genetic entity which carries information translatable by the cell.” (Benchmarks p. 341) “In general, students recognize the idea of species as a basis for classifying organisms, but few students will refer to the genetic basis of species.” NSES p.181 Essential Questions: Does evidence from the crime scene match with the suspects? Why must DNA be fragmented? Can this technology prove a person’s guilt or innocence? Behavioral Objective:

Students will focus on inquiry process, predicting experimental outcome, and evaluation of the data (gels).

Students will apply the basic principles of DNA fingerprinting. Description: This lab is used to determine who committed a crime by linking DNA evidence from a “crime scene” to DNA from several suspects. This lab is a spin-off from popular shows like CSI, which involves forensic testing. Students familiar with DNA, the use of restriction enzymes, and gel electrophoresis should be able to develop procedures to test and analyze the DNA provided. One 50- minute class period is required; some gels can be stained overnight and viewed the next day. Check kit recommendations. Inquiry Level: Level 2 if students use a pre-determined scenario and procedures. Level 3 inquiry if students develop their own scenario and procedures.








Materials: Bio-Rad “DNA Fingerprinting Kit” #166-0007EDU **Note: Some items contained in the kit need to be chilled or frozen upon arrival. 30-60 minutes of preparation are required before the lab period. Items not contained in the kit: P-20 micropipettes and tips Gel electrophoresis chambers and power supplies P-1000 micropipettes and tips DI water Microwave or hot plate Permanent markers Overhead sheets 250 mL and 500 mL Erlenmeyer flasks Ice bucket and ice Laboratory tape

Safety: Wear gloves and lab coats to avoid staining. Goggles should be worn at all times. Any chemical splash in the eyes should be flushed with water for a minimum of 15 minutes. Wash hands before and after lab. Food and drink should never be in the lab area.

Assessment: The Bio Rad kit contains lab question worksheets that can be used by students. A photo or tracing of DNA gels should be placed in the student lab notebook with a REE, PE, PA. Student evaluations can be made on correct technique or the presentation and evaluation of the evidence. Application: DNA fingerprinting has almost unlimited real-world applications. It can be used to identify individuals, indicate guilt or innocence of a crime, identify evolutionary linage, establish paternity, and detect genetically modified organisms and pathogenic organisms. T-Gen Lab: “DNA Chips: From Genes to Disease” Microarray Wet Lab (Llung cancer) www.genisphere.com Time Planned for activities: one 50 minute class period Prior Knowledge:

Students should be familiar with DNA microarrays. A good introduction is a computer simulation such as “Realistic Gene Chip Animation”:

http://gslc.genetics.utah.edu/units/biotech/microarray Students should understand the concepts of gene expression from transcription to create RNA and

translation or protein synthesis. General Concepts: DNA microarrays are a new technology that allows scientists to measure the activity (transcription) of thousands of genes simultaneously. All cells contain the same genes, but different genes are active in different types of cells. Genes do not have to be highly expressed to be of significance to a cell. A lack of gene expression, such as in a cancerous cell, could also be important. (T-Gen handout) Standards: NSES Content Standard A: Science as Inquiry Developing abilities and Understandings of Inquiry “Conceptual principles and knowledge guide scientific inquiries.” “Identify questions and concepts that guide scientific investigations.”

http://www.genisphere.com/

http://gslc.genetics.utah.edu/units/biotech/microarray



“Scientific explanations must adhere to criteria such as: a proposed explanation must be logically consistent; it must abide by the rules of evidence, it must be open to questions and possible modification; and it must be based on historical and current scientific knowledge.” NSES p.175 Content Standard C: Life Science The Molecular Basis of Heredity “Changes in DNA (mutations) occur spontaneously at low rates. Some of these changes make no difference to the organism, whereas others can change cells and organisms. Only mutations in germ cells can create the variation that changes an organism’s offspring.” NSES p.185 Content Standard G: History and Nature of Science Science as a Human Endeavor “Scientists are influenced by societal, cultural, and personal beliefs and ways of viewing the world. Science is not separate from society but rather science is a part of society.” NSES p.201 AZ State Standards: Science Standards

Strand 1: Concept 1: PO1 & PO2 Concept 2: PO1 & PO4

Strand 2: Concept 2: PO3 Misconceptions: “Students have a naïve view that the only important cancer genes are those that are highly expressed.” (T-Gen handout) Students have little understanding that new heritable characteristics are produced by chance…mutations of genes. (Benchmarks p. 343) Students of all ages will make casual inference even when no variation occurs in one of the variables. A basic problem understands the distinction between a variable making no difference and a variable that is correlated with an opposite outcome than the students conceived. (Benchmarks p. 340) Essential Questions: What is a microarray? How are gene chips created? What is a housekeeping gene? Why aren’t all genes expressed? How do genes prevent cancer? Behavioral Objectives:

Students will analyze gene expression and determine functional from inactive genes. Students will explain why all genes are not active and what a “housekeeping” gene does. Students will apply the basic principles of DNA microarray technology.

Description: Students will perform a wet lab that simulates real microarrays using inexpensive materials. Colors will vary from a real microarray (pinks, blues, and purples in this simulation). Materials are similar to an indicator lab. Student observations will be conceptually the same as a scientist using gene chip technology. Having students complete the virtual lab (link in prior knowledge) is highly recommended. Approximately 30 minutes is required for the virtual lab and an additional period for the wet lab and analysis. Inquiry Level: Level 1. As an introductory lesson on microarrays, the teacher needs to facilitate questions and discussion to check for conceptual understanding. Any further labs or activity could engage students in a higher level of inquiry. Students will be responsible for a summative explanation.







Materials: A “DNA gene chip” kit is commercially available. Additional needed materials are: Hot water bath for melting the agarose solutions. **Do not microwave! Bottles melt. Digital camera or colored pencils for documenting results / markers Approximately 30 minutes are needed to prep this lab.

Safety: The “cDNA” and “buffer” solutions contain a 0.4M NaOH solution. Designate one student per group to handle these reagents. Student should wear gloves and goggles. Any solution on skin should be washed with soap and water. Eyes should be flushed with water for 15 minutes in an eyewash station. Any surface spills should be wiped up immediately.

Assessment: Students must draw or photograph and attach results to lab notebook. Students will answer worksheet with teacher-made questions about the lab. *Teacher must lead a discussion or “check-in” with small groups to check for understanding and misconceptions. Students will answer an open-ended question in lab book about the experiment. Application and Real-World Connection: This lesson could be performed within a biotech, genetics, or DNA unit. Since microarrays are very expensive commercial pieces of equipment, this wet lab can be used to simulate expression, lack of expression, and varying degrees of expression. Students can learn the difference between “housekeeping genes” and what scientists would call “genes of interest”. This is best to perform before the paper and pencil activities for students to have prior knowledge about how scientists detect gene expression. Applications could be extended to biotechnology careers and exploration of bioinformatics. _____________________________________________________________________________________ Succeeding Unit: A comprehensive study of genetics will follow the biotechnology unit. The genetics unit will include Mendelian genetics, meiosis, and human genetics including human disease. A continued emphasis on biotechnology can be linked with “Genetic Screening of Newborn Infants” activity, “Baby Mice” activity, the “Huntington’s Disease” wet lab, and a virtual fieldtrip, “Recovering the Romanovs” on DNAi.org. The following content standards and concepts students should be able to understand from the above activities have been taken from the National Science Education Standards. Content Standard A: Science as Inquiry Developing Abilities to do Scientific Inquiry “Identify questions and concepts that guide scientific inquiry.” “Design and conduct scientific investigations.” “Formulate and revise scientific explanations and models using logic and evidence.” “Use technology and mathematics to improve investigations and communications.” “Recognize and analyze alternative explanations and models.” “Communicate and defend a scientific argument.” NSES p.175 Content Standard C: Life Science The Molecular Basis of Heredity “In all organisms, the instructions for specifying the characteristics of the organism are carried in DNA. The chemical and structural properties of DNA explain how the genetic information that underlies heredity is both encoded in genes and replicated. Each DNA molecule in a cell forms a single chromosome.” “Changes in DNA occur spontaneously at low rates. Some of these changes make no difference to the organism, whereas others can change cells and organisms.” NSES p.185





Biological Evolution “The great diversity of organisms is the result of more than 3.5 billion years of evolution that has filled every available niche with life forms.” “Natural selection and its evolutionary consequences provide a scientific explanation for the fossil record of ancient life forms, as well as for the striking molecular similarities observed among the diverse species of living organisms.” “The millions of different species of plants, animals, and microorganisms that live on Earth today are related by descent from common ancestors.” “Biological classifications are based on how organisms are related. Organisms are classified into a hierarchy of groups and subgroups based on similarities which reflect their evolutionary relationships. Species is the most fundamental unit of classification. NSES p.185 Matter, Energy, and Organization in Living Systems “The complexity and organization of organisms accommodates the need for obtaining, transforming, transporting, releasing, and eliminating the matter and energy used to sustain the organism.” NSES p.186 Content Standard F: Science in Personal and Social Perspectives Science and Technology in Local, National, and Global Challenges “Individuals and society must decide on proposals involving new research and the introduction of new technologies into society. Decisions involve assessment of risks, costs, and benefits and consideration of who benefits and who suffers, who pays, and who gains, and what the risks are and who bears them.” NSES p.199 Content Standard G: History and Nature of Science Science as a Human Endeavor “Scientists are influenced by societal, cultural, and personal beliefs and ways of viewing the world. Science is not separate from society but rather science is a part of society.” Historical Perspectives “Usually, changes in science occur as small modifications in extant knowledge. The daily work of science and engineering results in incremental advances in our understanding of the world and our ability to meet human needs and aspirations.” NSES p.201-204 Arizona State Science Standards Science Standards

Strand 1: Concept 1: PO1, PO2, PO3 & PO4 Concept 2 : PO1, PO2 & PO4

Strand 2: Concept 1 : PO1, PO3 & PO4 Strand 4: Concept 2: PO2 & PO3

Concept 4: PO1, PO5 & PO6 8th Grade Science Standards

Strand 3: Concept 2: PO4 APPENDIX www.DNAi.org “Recovering the Romanovs” Virtual field trip http://gslc.genetics.utah.edu/units/biotech/microarray Virtual microarray activity. www.genisphere.com “DNA Gene chip” wet lab. Click on “educational” tab.







http://azed.gov/standards/science/downloads/strand3.pdf

http://www.dnai.org/

http://gslc.genetics.utah.edu/units/biotech/microarray

http://www.genisphere.com/

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