Unit 1: Introduction and Lesson 6

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Unit 1 of 12: Lab Techniques & Data Analysis

Lesson 6 of 6: T ‐ Gen Lab: “DNA Chips: From Genes to Disease” Page 1 of 10

Unit 1: Introduction and Lesson 6

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 (

Lesson 3: pGLO lab ( 2 50 min periods)

Lesson 4: Dye Electrophoresis ( 1

Lesson 5: DNA Fingerprint Lab ( 1

1 50 min period)

50 min period)

50 min period)

Lesson 6: T-Gen Lab: “DNA Chips: From Genes to Disease”( 1 50 min period)

NAU BIOTECH © 2009 Michelle Landreville

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T-Gen Lab: “DNA Chips: From Genes to Disease”

Microarray Wet Lab (Lung cancer) www.genisphere.com

Time Planned for activities: one 50 minute class period

Prior Knowledge:

9 Students should be familiar with DNA microarrays.

9

A good introduction is a computer simulation such as “Realistic Gene Chip Animation”: http://gslc.genetics.utah.edu/units/biotech/microarray

9 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.”

“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)


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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:

9

Students will analyze gene expression and determine functional from inactive genes.

9

Students will explain why all genes are not active and what a “housekeeping” gene does.

9

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.

_______________________________________________________________________


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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.”


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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.


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NAU BIOTECH




NAU BIOTECH




NAU BIOTECH




NAU BIOTECH




Unit 1: Introduction and Lesson 6

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