Lesson 2.1 Diving into DNA PDF

Lesson 2.1 Diving into DNA Preface Deoxyribonucleic acid (DNA) is the target of many biotechnological applications. To study DNA it must be extracted from the cell. DNA extraction can be a fairly simple process using household chemicals to break down the cell membranes and extract DNA. Once is...

Lesson 2.1 Diving into DNA Preface Deoxyribonucleic acid (DNA) is the target of many biotechnological applications. To study DNA it must be extracted from the cell. DNA extraction can be a fairly simple process using household chemicals to break down the cell membranes and extract DNA. Once isolated, DNA can be digested using restriction enzymes and used in forensic analysis. In this lesson, students will write procedures to extract DNA, prepare agarose gel trays for electrophoresis, observe the migration patterns of dyes, and use restriction enzymes to digest lambda DNA and observe the differences using Restricted Fragment Length Polymorphism. They will then solve a problem using techniques learned in this lesson to determine the culprit of a crime. Concepts Performance Objectives Students will know and understand Students will learn concepts by doing 1. DNA is extracted from cellular matter to be · Write an experiment to extract DNA from kiwi studied. fruit. (Project 2.1.1) · Extract DNA from kiwi fruit using procedures developed. (Project 2.1.1) · Mix solutions and pour gel trays to prepare agarose gels. (Activity 2.1.2) · Conduct gel electrophoresis to observe the migration of dyes and extracted DNA. (Activity 2.1.3) 2. Restriction enzymes are used to cut DNA in · Demonstrate the action of restriction enzymes order to compare organisms, isolate and using paper DNA strands. (Activity 2.1.4) transfer genes, and genetically modify organisms. 3. DNA profiles are created using fragments · Digest a DNA sample using restriction produced through Restriction Fragment Length enzymes and conduct gel electrophoresis to Polymorphism. analyze the results. (Activity 2.1.5) · Solve a problem determining the culprit of a crime using restriction enzymes and gel electrophoresis. (Problem 2.1.6) National AFNR Common Career Technical Core Standards Alignment Biotechnology Systems Career Pathway Content Standards BS.02: Demonstrate proficiency by safely applying appropriate laboratory skills to complete tasks in a biotechnology research and development environment (e.g., standard operating procedures, record keeping, aseptic technique, equipment maintenance, etc.). · BS.02.03: Apply standard operating procedures for the safe handling of biological and chemical materials in a laboratory. · BS.02.05: Examine and perform scientific procedures using microbes, DNA, RNA and proteins in a laboratory. Next Generation Science Standards Alignment Disciplinary Core Ideas Life Science LS1: From Molecules to Organisms: Structures and Processes · Systems of specialized cells within organisms help them perform the essential functions of LS1.A: Structure life. and Function · All cells contain genetic information in the form of DNA molecules. Genes are regions in the DNA that contain the instructions that code for the formation of proteins, which carry out most of the work of cells. LS3: Heredity: Inheritance and Variation of Traits · Each chromosome consists of a single very long DNA molecule, and each gene on the LS3.A: Inheritance chromosome is a particular segment of that DNA. The instructions for forming species’ of Traits characteristics are carried in DNA. All cells in an organism have the same genetic content, but the genes used (expressed) by the cell may be regulated in different ways. Not all DNA codes for a protein; some segments of DNA are involved in regulatory or structural functions, and some have no as-yet known function. LS4: Biological Evolution: Unity and Diversity · Genetic information provides evidence of evolution. DNA sequences vary among species, but LS4.A: Evidence there are many overlaps; in fact, the ongoing branching that produces multiple lines of descent of Common can be inferred by comparing the DNA sequences of different organisms. Such information is Ancestry and also derivable from the similarities and differences in amino acid sequences and from Diversity anatomical and embryological evidence. Science and Engineering Practices Asking Asking questions and defining problems in 9–12 builds on K–8 experiences and progresses to Questions and formulating, refining, and evaluating empirically testable questions and design problems using Defining models and simulations. Problems · Ask questions that arise from careful observation of phenomena, or unexpected results ▪ to clarify and/or seek additional information. ▪ that arise from examining models or a theory, to clarify and/or seek additional information and relationships. ▪ to determine relationships, including quantitative relationships, between independent and dependent variables. ▪ to clarify and refine a model, an explanation, or an engineering problem. · Ask questions that can be investigated within the scope of the school laboratory, research facilities, or field (e.g., outdoor environment) with available resources and, when appropriate, frame a hypothesis based on a model or theory.  Planning and Planning and carrying out investigations in 9-12 builds on K-8 experiences and progresses to Carrying Out include investigations that provide evidence for and test conceptual, mathematical, physical, Investigations and empirical models. · Plan an investigation or test a design individually and collaboratively to produce data to serve as the basis for evidence as part of building and revising models, supporting explanations for phenomena, or testing solutions to problems. Consider possible confounding variables or effects and evaluate the investigation’s design to ensure variables are controlled. · Select appropriate tools to collect, record, analyze, and evaluate data. · Make directional hypotheses that specify what happens to a dependent variable when an independent variable is manipulated. · Manipulate variables and collect data about a complex model of a proposed process or system to identify failure points or improve performance relative to criteria for success or other variables. Constructing Constructing explanations and designing solutions in 9–12 builds on K– 8 experiences and Explanations and progresses to explanations and designs that are supported by multiple and independent Designing student-generated sources of evidence consistent with scientific ideas, principles, and theories. Solutions · Make a quantitative and/or qualitative claim regarding the relationship between dependent and independent variables. Crosscutting Concepts Patterns Observed patterns in nature guide organization and classification and prompt questions about relationships and causes underlying them. · Different patterns may be observed at each of the scales at which a system is studied and can provide evidence for causality in explanations of phenomena. · Classifications or explanations used at one scale may fail or need revision when information from smaller or larger scales is introduced; thus requiring improved investigations and experiments. Scale, Proportion, In considering phenomena, it is critical to recognize what is relevant at different size, time, and Quantity and energy scales, and to recognize proportional relationships between different quantities as scales change. · Some systems can only be studied indirectly as they are too small, too large, too fast, or too slow to observe directly. Systems and A system is an organized group of related objects or components; models can be used for System Models understanding and predicting the behavior of systems. · Systems can be designed to do specific tasks. · When investigating or describing a system, the boundaries and initial conditions of the system need to be defined and their inputs and outputs analyzed and described using models. Understandings about the Nature of Science Scientific · Science investigations use diverse methods and do not always use the same set of Investigations Use a procedures to obtain data. Variety of Methods · Scientific inquiry is characterized by a common set of values that include: logical thinking, precision, open-mindedness, objectivity, skepticism, replicability of results, and honest and ethical reporting of findings. · Scientific investigations use a variety of methods, tools, and techniques to revise and produce new knowledge. Science is a Way of · Science is both a body of knowledge that represents a current understanding of natural Knowing systems and the processes used to refine, elaborate, revise, and extend this knowledge. Common Core State Standards for High School Mathematics Modeling standards are indicated by the star symbol (*) throughout other conceptual categories. CCSS: Conceptual Category – Number and Quantity Quantities · *Reason quantitatively and use units to solve problems. CCSS: Conceptual Category – Algebra Seeing Structure in · *Interpret the structure of expressions. Expressions · *Write expressions in equivalent forms to solve problems. Arithmetic with · Perform arithmetic operations on polynomials. Polynomials and Rational Expressions Creating Equations · *Create equations that describe numbers or relationships. Reasoning with Equations · Understand solving equations as a process of reasoning and and Inequalities explain the reasoning. · Solve equations and inequalities in one variable. Common Core State Standards for English Language Arts CCSS: English Language Arts Standards » Science & Technical Subjects » Grade 11-12 Key Ideas and Details · RST.11-12.2 – Determine the central ideas or conclusions of a text; summarize complex concepts, processes, or information presented in a text by paraphrasing them in simpler but still accurate terms. Range of Reading and · RST.11-12.10 – By the end of grade 12, read and comprehend science/technical Level of Text texts in the grades 11-CCR text complexity band independently and proficiently. Complexity CCSS: English Language Arts Standards » Writing » Grade 11-12 Production and · WHST.11-12.4 – Produce clear and coherent writing in which the development, Distribution of organization, and style are appropriate to task, purpose, and audience. Writing · WHST.11-12.5 – Develop and strengthen writing as needed by planning, revising, editing, rewriting, or trying a new approach, focusing on addressing what is most significant for a specific purpose and audience. Research to Build · WHST.11-12.7 – Conduct short as well as more sustained research projects to and Present answer a question (including a self-generated question) or solve a problem; narrow or Knowledge broaden the inquiry when appropriate; synthesize multiple sources on the subject, demonstrating understanding of the subject under investigation. Range of Writing · WHST.11-12.10 – Write routinely over extended time frames (time for reflection and revision) and shorter time frames (a single sitting or a day or two) for a range of discipline-specific tasks, purposes, and audiences. Essential Questions  1. How is DNA extracted from a cell? 2. Why does DNA need to be extracted from a cell? 3. How is agarose different from agar? 4. How do I prepare a 1x solution from a 50x solution? 5. Why is a comb necessary in the gel tray? 6. Why is a Tris/acetic acid/EDTA buffer used in electrophoresis instead of water? 7. How does gel electrophoresis work? 8. What color dye moves the furthest during electrophoresis? 9. How can you predict where a restriction enzyme will cut DNA? 10. How many times can a restriction enzyme cut a strand of DNA? 11. What is a lambda bacteria phage? 12. How is Restriction Fragment Length Polymorphism used in biotechnology? 13. What are applications of gel electrophoresis? Key Terms Agarose Bacteriophage Buffer Cell biology Chemistry DNA size standard EDTA Electrode Electrophoresis Extract Lambda DNA Lysis Protocol Restriction enzyme RFLP Sample loading TAE buffer TE buffer buffer Tris Day-to-Day Plans Time: 13 days The teacher will refer to the Teacher Resources section for specific information on teaching this lesson, in particular Lesson 2.1 Teacher Notes, Lesson 2.1 Glossary, Lesson 2.1 Materials, and other support documents. Day 1 – 3: · The teacher will present Concepts, Performance Objectives, Key Terms, and Essential Questions in order to provide a lesson overview. · The teacher will review the reading assignment for Chapter 4 pages 105-113 using the discussion questions provided in Lesson 2.1 Teacher Notes.  · The teacher will provide students with a copy of Project 2.1.1 DNA Extraction Protocol. · Students will work in pairs to complete Project 2.1.1 DNA Extraction Protocol. · The teacher will use Project 2.1.1 Evaluation Rubric to assess student protocol and projects. Day 4: · The teacher will briefly review the assigned reading and facilitate a class discussion. · The teacher will provide students with a copy of Activity 2.1.2 Agarose Gels. · Students will work in pairs to complete Activity 2.1.2 Agarose Gels. Day 5: · The teacher will provide students with a copy of Activity 2.1.3 Electrophoresis Currents. · Students will work in pairs to complete Activity 2.1.3 Electrophoresis Currents. Day 6: · The teacher will provide students with a copy of Activity 2.1.4 Cutting Up DNA. · The students will work in pairs to complete Activity 2.1.4 Cutting Up DNA. · The teacher will provide students with a copy of Activity 2.1.5 Dicing Lambda DNA. · Students will work individually to complete Part One – Pre-Lab Research for Activity 2.1.5 Dicing Lambda DNA. Day 7: · Students will work in pairs to complete Part Two of Activity 2.1.5 Dicing Lambda DNA. Day 8: · Students will work in pairs to complete Part Three of Activity 2.1.5 Dicing Lambda DNA. Day 9: · Students will work in pairs to complete Part Four of Activity 2.1.5 Dicing Lambda DNA. Day 10 – 12: · The teacher will provide students with a copy of Problem 2.1.6 The Chewed Shoe and Guide to Assessing Problems. · Student will work in pairs to solve Problem 2.1.6 The Chewed Shoe. Day 13:  · The teacher will assess student methods and procedures for Problem 2.1.6 The Chewed Shoe using the Guide to Assessing Problems. · The teacher will distribute Lesson 2.1 Check for Understanding. · Students will complete Lesson 2.1 Check for Understanding and submit for grading. · The teacher will use Lesson 2.1 Check for Understanding Answer Key to grade student assessments. · READING: Students will read Chapter 5 of the course text, Biotechnology: A Laboratory Skills Course, in preparation for the coming lesson. Instructional Resources Student Support Documents Lesson 2.1 Glossary Project 2.1.1 DNA Extraction Protocol Activity 2.1.2 Agarose Gels Activity 2.1.3 Electrophoresis Currents Activity 2.1.4 Cutting Up DNA Activity 2.1.5 Dicing Lambda DNA Problem 2.1.6 The Chewed Shoe Teacher Resources Lesson 2.1 Teacher Notes Lesson 2.1 Check for Understanding Lesson 2.1 Materials Answer Keys and Assessment Rubrics Project 2.1.1 Evaluation Rubric Lesson 2.1 Check for Understanding Answer Key Guide to Assessing Problems Reference Sources Bio-Rad Laboratories, Inc. (n.d.). Forensic DNA Fingerprinting Kit Instruction Manual. Hercules, CA: Author. Brown, J. K. (2011). Biotechnology: A laboratory skills course. Hercules, CA: Bio-Rad Laboratories, Inc. Daugherty, E. (2007). Biotechnology: Science for a new millennium. St. Paul, MN: Paradigm Publishing, Inc.  Dictionary.com Unabridged. (2015). Retrieved from http://dictionary.reference.com/browse/protocol Farlex Partner Medical Dictionary. (2012). Retrieved from http://medical-dictionary.thefreedictionary.com Herren, R. V., & Donahue, R. L. (2000). Delmar’s agriscience dictionary with searchable CD-ROM. Albany, NY: Delmar. Kreuzer, H., & Massey, A. (1996). Recombinant DNA and biotechnology. Washington D.C.: American Society for Microbiology. This lesson will provide conceptual and procedural knowledge required for participation in the following FFA activities: · Agricultural Research and Emerging Agricultural Technology Proficiency Areas · Agriscience Fair · Agricultural Issues Forum Career Development Event For more on the National FFA Organization review the following URL: http://www.ffa.org/. Laboratory and research skills are highly sought after in the workforce. Below are some examples of SAE activities connected to this lesson of study: · Internships or part-time jobs at local businesses utilizing laboratory and research skills. · Develop research projects using the applications of DNA technology practiced in this lesson. For more information regarding opportunities related to Supervised Agricultural Experience, view the webpage at the following URL: https://www.ffa.org/about/supervised-agricultural-experiences. Critical Thinking and Application Extensions Explanation 1. Students will write a one-page essay describing the applications of DNA extraction, restriction enzymes, and DNA fingerprinting in plant and animal agriculture. 2. Students will participate in a debate pertaining to the accuracy of DNA fingerprinting and the potential errors that may occur in the process. Application 3. Students will develop a protocol for utilizing DNA fingerprinting in a common agricultural application and conduct tests of the accuracy and usefulness of their protocol.