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Cells, Genetics
                      and
                Biotechnology
 •   Cell Factories

 •   Cell Dissection

 •   Pi...
Designers, editors, and contributors


Sujaya Rao, editor and director, Rural Science Education Program (Associate Profess...
Lesson 1

                                         Cell Factories


Objective:
      Students will understand how the orga...
CELL FACTORY ASSESSMENT FORM – Please fill out a form for yourself.

Evaluation of:



    1. Project exhibits understandi...
Comments: ________________________________________________________

______________________________________________________...
Reference Material on Cellular Organelles
Membrane - The major barrier of the cell, separating the inside of the cell from...
Ribosome - Ribosomes are responsible for assembling the proteins of the cell. Ribosomal
subunits are synthesized by the nu...
Animal Cell

                                                Plant Cell




                                      Types of...
Lesson 2

                                        Cell Dissection

       Adapted from: http://www.askeric.org/Virtual/Les...
Plant Cell
    Organelle                Ingredient
    Membrane                 Plastic baggie
    Cytoplasm              ...
Lesson 3

                                     Pipe cleaner Mitosis


Objective: To understand mitosis by making a model o...
Reference material

                                Stages of the cell cycle

http://bhs.smuhsd.org/bhsnew/academicprog/sc...
From: http://www.rpgroup.caltech.edu/courses/aph162/2006/webpages/Projects/Alex-JinHong-
Eileen/index.html

Interphase

  ...
Telophase

              Chromatids arrive at opposite poles of cell, and new membranes form around the
              daug...
Reference material
                                     Chromosomes
http://www.micro.utexas.edu/courses/levin/bio304/genet...
http://www.cbs.dtu.dk/staff/dave/roanoke/genetics980218.html
Stages of Mitosis

http://www.bbc.co.uk/schools/gcsebitesize/biology/cellprocesses/celldivisionrev2.shtml
Lesson 4
                                      Marshmallow Meiosis


                        Based on http://www.iloveteac...
2.   This activity seemed to work best in pairs or groups of three. Each pair would create one
        set of gametes and ...
Marshmallow Meiosis – Handout                  Name:
                                                                     ...
You have been given a representation of both the female and male Reebop chromosome sets. It

is your mission to create gam...
1   AA         1 antenna

1   Aa         2 antenna         Incomplete Dominance

1   aa         No antenna

2   MM        ...
Handout
                                  Stages of Meiosis


http://www.bbc.co.uk/schools/gcsebitesize/biology/cellproces...
Lesson 5

                              Transcription and Translation
                                    DNA to Protein

...
•   Initiation codon: a codon (AUG) that begins the translation process from messenger
       RNA to protein

   •   Termi...
As the codon              As the anti-codon
CCC   Proline                   Glycine
CCU   Proline                   Glycin...
From: http://www-stat.stanford.edu/~susan/courses/s166/node2.html




NSF GK-12 Rural Science Education Program, Oregon St...
http://allserv.rug.ac.be/~avierstr/principles/pcr.html




NSF GK-12 Rural Science Education Program, Oregon State Univers...
Lesson 6

                                 Animal Genetics
Objective:
  • Students will understand how Punnett Squares wor...
•   Incomplete dominance – both alleles are responsible for resulting phenotype. RR
        = red, Rr = pink, rr = white.
...
Sample Student Worksheet- Cats


 Name: ______________________

 Fill in the missing information for each trait. After you...
Incomplete Dominance Traits
Trait #5: Nose Color
In this case, each genotype produces a different phenotype since the domi...
Lesson 7

                                   Fruit Fly Ranching
…
    Student Outcomes/Objectives
       • to gain a bette...
Fruit Fly Ranching


                           Fruit Fly Ranch Activity

Procedures

   1. This is a culminating inquiry-...
7. After the growing medium has been prepared, the students will now wait for their flies to
      grow. Every couple of d...
Fruit Fly Ranch Loan Paperwork




Date:     _______

Regarding: Loan for          (Ranch Name)

Dear Mr. / Ms.           ...
Name ___________________


                     My Fruit Fly Ranch

Date           Activity      Income   Expenses       B...
Example Result Form
                     Tax    Tax                                        Net
                     Rate  ...
Lesson 8

                                       DNA Extraction

Objective:
Students will learn how to extract DNA from li...
2. Mix macerated sample with a pinch of salt and tap water (2x the volume of the sample)
      to create a “cell soup”.
  ...
Name____________________________
                                                            Date_________________________...
c. How does this help DNA replicate?




6. What is the difference between DNA and RNA?




7. What is a chromosome?



8....
Teacher Copy
                                                            Name____________________________
                ...
c. How does this help DNA replicate?

          Unwound strands of DNA reveal a single strand of nucleotides which serve a...
Lesson 9

                                     Gel Electrophoresis

        Protocol for Pouring, Loading, and Running a D...
11. Check for bubbles and use a pipette tip to pop any found
12. Let solidify (~30 minutes depending on the size of the ge...
Loading a Gel

Materials

   •   Solidified Gel
   •   Electrophoresis
   •   1X TBE
   •   DNA Samples
   •   Standard


...
Running a Gel

1. Place the top of the electrophoresis unit onto the box making sure that the contacts are

    appropriat...
will become increasingly distinct as gel destains. You may continue to destain

         overnight in a small volume of wa...
Figure from: http://en2.wikipedia.org/wiki/Agarose_gel_electrophoresis


(1) The agarose gel with three slots (S).
(2) Inj...
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Transcript of "Cells, Genetics and Biotechnology"

  1. 1. Cells, Genetics and Biotechnology • Cell Factories • Cell Dissection • Pipe cleaner Mitosis • Marshmallow Meiosis • Transcription and Translation • Animal Genetics • Fruit Fly Ranching • DNA Extraction • Gel Electrophoresis Rural Science Education Program A partnership between Oregon State University and rural K-12 schools
  2. 2. Designers, editors, and contributors Sujaya Rao, editor and director, Rural Science Education Program (Associate Professor of Entomology) Joy Waite, author (Graduate Fellow, Rural Science Education Program) Sarah Gehlhar, author, (Graduate Fellow, Rural Science Education Program) Anne Halgren, author, (Graduate Fellow, Rural Science Education Program) Eryn Cramer, author, (Undergraduate Fellow, Rural Science Education Program) Denise Baumann, author, (Undergraduate Fellow, Rural Science Education Program) Jeff McGarvey, author (Science Teacher, Alsea School, Oregon) Sylvia Harvey, author (Science Teacher, Seven Oak Middle School, Oregon) Kathy Brandis, author (Science Teacher, Seven Oak Middle School, Oregon) Rural Science Education Program The Rural Science Education Program is a partnership between Oregon State University and local rural K-12 schools for enrichment of the science curriculum with hands-on science activities that encourage critical thinking in K-12 students about the impacts of agriculture on the environment and the implications of advanced scientific research on human lives. For More Information For more information about the Rural Science Education Program, contact Sujaya Rao (phone: (541) 737-9038; e-mail: sujaya@oregonstate.edu; fax: (541) 737-5725. This material is based upon work supported by the National Science Foundation and Toshiba America Foundation. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and the editor, and do not necessarily reflect the views of the National Science Foundation or Toshiba America Foundation.
  3. 3. Lesson 1 Cell Factories Objective: Students will understand how the organelles work together within a cell. Students will design a factory that is analogous to a cell and its organelles. Grade Level- 8-12 National Standards: • Students should develop an understanding of structure and function in living systems • Students should develop understanding of the cell Background Knowledge: Students should have a basic understanding of cell organelles. Materials: • craft supplies • cardboard • construction paper • glue • reference materials on cell organelles Procedure: 1. Students work in groups of four. 2. Each group chooses a product that could be produced in a factory (it can be real or imaginary) 3. Using the reference materials as guides, groups create a model of the factory that makes their product. They must assign each aspect of the factory process to an organelle. 4. Once the factory is completed each group must write an explanation of how the various factory parts are analogous to the organelles the group chooses. 5. Each group presents their factory to the class. 6. Each student completes their own assessment form about the project.
  4. 4. CELL FACTORY ASSESSMENT FORM – Please fill out a form for yourself. Evaluation of: 1. Project exhibits understanding of cell structure and function. 1 2 3 4 5 very little Somewhat adequately accomplished distinguished 2. Project implies importance of the cellular organelles. 1 2 3 4 5 very little Somewhat adequately accomplished distinguished 3. Project displays appropriate analogies. 1 2 3 4 5 very little Somewhat Adequately accomplished distinguished 4. Cell factory is efficient. 1 2 3 4 5 very little Somewhat adequately accomplished distinguished 5. Group was well prepared for their presentation. 1 2 3 4 5 very little Somewhat adequately accomplished distinguished 6. The project was original and creative. 1 2 3 4 5 Very little Somewhat adequately accomplished distinguished 7. The presentation kept my attention. 1 2 3 4 5 very little Somewhat adequately accomplished distinguished 8. Overall quality of project. 1 2 3 4 5 Very little Somewhat adequately accomplished distinguished
  5. 5. Comments: ________________________________________________________ __________________________________________________________________ __________________________________________________________________ EFFORT: __Excellent __Very Good __Fair __I/group/individual could have done better ASSESSMENT POINTS Points Possible Self Instructor 1. subject researched (10) ____ ____ 2. project completed on time (10) ____ ____ 3. worked as a group (10) ____ ____ 4. creation of a useful learning tool (10) ____ ____ 5. worked as an individual (10) ____ ____ Likes / Dislikes of Project: __________________________________________________________________ __________________________________________________________________ Suggestions to improve: __________________________________________________________________ __________________________________________________________________
  6. 6. Reference Material on Cellular Organelles Membrane - The major barrier of the cell, separating the inside of the cell from the outside. It is this structure that allows cells to selectively interact with their environment. Cytoplasm – A material that lies within the cytoplasmic membrane and holds everything in a cell outside of the nucleus. Cytoplasm contains a lot of water and the other organelles of the cell. It is made up of proteins, vitamins, ions, nucleic acids, amino acids, sugars, carbohydrates and fatty acids. All of the functions for cell expansion, growth and replication are carried out in the cytoplasm of a cell. Cell wall – A rigid supporting wall located exterior to the plasma membrane in plants and bacteria Mitochondria – Spherical or elongated intracellular organelles that contain the electron transport system and enzymes. They are often referred to as the “powerhouse” of the cell and contain the molecular machinery for the conversion of sugar to energy. Chloroplast – chlorophyll bearing intra-cellular organelle of plant cells. Chloroplasts are the site of photosynthesis. Vacuole – A membrane bound sac found within the cytoplasm. It functions in storage, digestion, transport, and water elimination. Plant cells contain a very large vacuole that plays an important role in maintaining turgor pressure. Nucleus – The spherical cellular organelle that contains DNA and serves as the control center of the cell Endoplasmic reticulum (ER) – A 3-dimensional maze of connecting and branching channels made by a continuous membrane. The ER is responsible for segregation of proteins destined for export from the cell or for intracellular use as well as, steroid synthesis, metabolism and detoxification of substances in the liver just to name a few functions. Golgi apparatus – Organelle composed of stacks of flattened membranous sacs. The Golgi is mainly responsible for modifying, packaging, and sorting proteins. Lysosome – Small round structure involved in the digestive activities of the cell in order to break down food items for use by the mitochondria for energy. DNA – Deoxyribonucleic acid (DNA) is present in a cells chromosomes and contains the genetic information for the living organism.
  7. 7. Ribosome - Ribosomes are responsible for assembling the proteins of the cell. Ribosomal subunits are synthesized by the nucleolus. They generally exist in the cytoplasm and bound to the ER.
  8. 8. Animal Cell Plant Cell Types of Cells Source : http://www.physicalgeography.net/fundamentals/6a.html
  9. 9. Lesson 2 Cell Dissection Adapted from: http://www.askeric.org/Virtual/Lessons/Science/Biology/BIO0035.html Objective: Students will recognize differences between prokaryote, plant, and animal cells. Students will be able to create a data table to explain the differences. National Standards: • Students should develop an understanding of structure and function in living systems • Students should develop understanding of the cell Background Knowledge: Students must be introduced to the concept that plants, animals, and prokaryotes are all made of cells. The three cell types have different structures, components, and functions making each cell type unique. The different organelles should be introduced and their different functions explained. Materials Needed: • 4 colors of Jell-O – 1 box/cell • Various candies or objects to represent cellular organelles – see below under Plant and Animal Cell • Plastic bags with twist ties • Plastic plates • Plastic knives • Plastic spoons • Gloves • Graph Paper Procedure: A. Ahead of time (Another class could do the preparation) a. Prepare cells as described below. b. Mix Jell-O as directed for “Jigglers” on box c. Fill plastic baggies with Jell-O, leaving only enough room to close bag. Allow Jell-o to start to set, but do not allow to completely set. d. Insert “organelles” (example: ribosome = beads, mitochondria = mandarin oranges, etc.) e. Place plant and prokaryotic cells in small loaf pans to create a standard shape and allow animal cells to free form. f. Close “cells” and allow to set in refrigerator several hours or overnight
  10. 10. Plant Cell Organelle Ingredient Membrane Plastic baggie Cytoplasm Jell-O (color #1) Cell Wall Jell-O (color #4 in another bag around 1st Jell-O bag)* Mitochondria Mandarin Orange Segments Chloroplast Green jellybeans Vacuole Giant jawbreaker Nucleus Gumball Endoplasmic Ramen Noodles (dry) Reticulum Golgi Apparatus Licorice Ribbon Animal Cell Organelle Ingredient Membrane Plastic baggie Cytoplasm Jell-O (color #2) Mitochondria Mandarin Orange Segments Nucleus Gumball Endoplasmic Reticulum Ramen Noodles (dry) Golgi Apparatus Licorice Ribbon Secretory Vesicles Mini Chewy Sweetarts B. Class a. Handout instructions and assignment for lab and explain the process of dissection and the safety issues involved b. Divide students into groups of two • assign one partner as the dissector • assign the other as a recorder c. Distribute a plastic knife, spoon, and plate to each group d. Distribute a “Jell-O cell” to each pair e. Allow students to dissect the cells and remind them to keep careful record of everything they find (repeat for as many cell types as you want each group to dissect) f. Clean up the cells and their organelles g. Get pairs back together and allow them to work on organizing their observations into a data chart. (i.e. What did they find?, How many were in the cell?, What could the ingredient have represented?, etc.) h. With their data chart complete and comparing to the diagrams given, can the students make an inference as to what kind of cell they dissected (plant, animal, prokaryote)? i. Have the students hand in an organized data chart and a paragraph about their inferences as a lab write-up. NSF GK-12 Rural Science Education Program, Oregon State University http://cropandsoil.oregonstate.edu/gk12
  11. 11. Lesson 3 Pipe cleaner Mitosis Objective: To understand mitosis by making a model out of pipe-cleaners National Standards: • Students should develop an understanding of reproduction and heredity • Students should develop understanding of molecular basis of heredity Background Knowledge: Students should have a basic understanding of cell organelles. Materials: • Pipe cleaners of various colors • String • Reference materials – Stages of Cell Cycle, Chromosomes, Stages of Mitosis Procedure: Step 1- Take 2 pipe-cleaners of several colors each (=Chromosomes) and two pieces of string (=cell membrane) Step 2- Drop one set of the pipe-cleaners in a pile and place the string to form a circle around the pile then add the other set to duplicate the chromosomes-this is INTERPHASE Step 3- Pair up the colors- these are your sister chromatids in PROPHASE Step 4- Twist pipe-cleaners together in pairs- these represent your chromosomes at PROMETAPHASE Step 5- Line up the twisted pipe-cleaners along the centerline-this is METAPHASE Step 6- Untwist the pipe-cleaners and pull one of each color to opposite ends of your cell-this in ANAPHASE Step 7- Bring the end of the string together to form two circles touching each other and placing one set of each color pipe-cleaner in each-this is TELOPHASE Step 8- Separate the circles with the pipe-cleaners-this is CYTOKINESIS the final step to make two identical cells!
  12. 12. Reference material Stages of the cell cycle http://bhs.smuhsd.org/bhsnew/academicprog/science/vaughn/Student%20Projects/Paul%20&%2 0Marcus/Cell_Replication.html
  13. 13. From: http://www.rpgroup.caltech.edu/courses/aph162/2006/webpages/Projects/Alex-JinHong- Eileen/index.html Interphase The cell is engaged in metabolic activity and preparing for mitosis (the next four phases that lead up to and include nuclear division). Chromosomes are not clearly discerned in the nucleus, although a dark spot called the nucleolus may be visible. The cell may contain a pair of centrioles (or microtubule organizing centers in plants) both of which are organizational sites for microtubules. 90% of Mitosis occurs in this stage. Prophase Chromatin in the nucleus begins to condense and becomes visible in the light microscope as chromosomes. The nucleolus disappears. Centrioles begin moving to opposite ends of the cell and fibers extend from the centromeres. Some fibers cross the cell to form the mitotic spindle. Prometaphase The nuclear membrane dissolves, marking the beginning of prometaphase. Proteins attach to the centromeres creating the kinetochores. Microtubules attach at the kinetochores and the chromosomes begin moving. Metaphase Spindle fibers align the chromosomes along the middle of the cell nucleus. This line is referred to as the metaphase plate. This organization helps to ensure that in the next phase, when the chromosomes are separated, each new nucleus will receive one copy of each chromosome. Anaphase The paired chromosomes separate at the kinetochores and move to opposite sides of the cell. Motion results from a combination of kinetochore movement along the spindle microtubules and through the physical interaction of polar microtubules.
  14. 14. Telophase Chromatids arrive at opposite poles of cell, and new membranes form around the daughter nuclei. The chromosomes disperse and are no longer visible under the light microscope. The spindle fibers disperse, and cytokinesis or the partitioning of the cell may also begin during this stage. Cytokinesis In animal cells, cytokinesis results when a fiber ring composed of a protein called actin around the center of the cell contracts pinching the cell into two daughter cells, each with one nucleus. In plant cells, the rigid wall requires that a cell plate be synthesized between the two daughter cells.
  15. 15. Reference material Chromosomes http://www.micro.utexas.edu/courses/levin/bio304/genetics/genetics.html Chromosome: The self replicating genetic structures of cells containing the cellular DNA that carries its nucleotide sequence (linear array of genes). Homologous chromosomes: Chromosomes that match in size and shape. A pair of genes containing the same linear gene sequence, each derived from one parent. Sister chromatids: Chromatids derived from the same chromosome that still share the same centromere. Centromere: Area in a chromosome where spindle fibers are attached to move the chromosome during cell division. This is usually a constricted area of the chromosome called the “primary constriction.” Mitosis: The process of nuclear division in cells that produces daughter cells that are genetically identical to each other and to the parent cell. Meiosis: A two stage type of cell division in sexually reproducing organisms that results in gametes with half the chromosome number in the original cell.
  16. 16. http://www.cbs.dtu.dk/staff/dave/roanoke/genetics980218.html
  17. 17. Stages of Mitosis http://www.bbc.co.uk/schools/gcsebitesize/biology/cellprocesses/celldivisionrev2.shtml
  18. 18. Lesson 4 Marshmallow Meiosis Based on http://www.iloveteaching.com/writesci/Rebops/ Objective: To explore the process of meiosis from chromosome segregation and gamete formation to gamete recombination to determination of genotype and resulting phenotype. National Standards: • Students should develop an understanding of reproduction and heredity • Students should develop understanding of molecular basis of heredity Background knowledge: Students should have a general understanding of the difference between meiosis and mitosis and what the purpose of each is. Students should also have knowledge of what an allele is and a basic grasp on the terms genotype and phenotype as well as the idea of inheritance. Other helpful background knowledge would include familiarity with the terms heterozygous and homozygous. Materials needed: • Set of chromosomes made from colored paper o Male (Green) & Female (Yellow) 32 strips of paper total (4 each - 11, 10, 8, 5, 4, 3, 2, &1” long x 1”wide) – divide into two matching sets (2 of each length). Both parents are heterozygous so write one capital letter and one small letter on each pair of chromosomes; make two identical sets. A a Q q E e D d M m T t L l X X Create two or heterozygous Y chromosome sets for each the male and female – 4 • Large marshmallows (body and head) sets total. • Small colored marshmallows (humps, nose) • Colored toothpicks (ligaments/bones, legs, antenna) • Pipe-cleaners (tails) • Thumb tacks (eyes) • Handouts – Marshmallow Meiosis, Stages of Meiosis Procedures: 1. Prepare the chromosome sets or if the class is advanced enough they can make their own.
  19. 19. 2. This activity seemed to work best in pairs or groups of three. Each pair would create one set of gametes and then depending if they had a male or a female they would search out a Reebop of the opposite sex to mate with. 3. Depending on the student’s level of understanding and knowledge of meiosis it may be helpful to provide the students with a diagram of meiosis that they can follow along. 4. Begin the activity by explaining how these new creatures called “Reebops” have been discovered. They have 8 chromosomes (2n=16) and are diploid just like humans (2n=46). 5. You have been fortunate enough to capture 2 heterozygous Reebops; one male and one female. It is the student’s job to simulate meiosis for these two parents and determine what their progeny may look like. 6. The students will then use the heterozygous set of chromosomes you have made to practice the process of meiosis and create four gametes for their Reebop. After creating the four gametes they each pick one and discard the rest (push to the side of the table). Have the students record their set of alleles. 7. Then they need to find a Reebop gamete of the opposite sex to combine with. After they acquire this information they can determine their genotype and from that determine the phenotype of their Reebop using the secret decoding chart. 8. After they have determined the phenotype allow the students to construct their baby Reebop using marshmallows, toothpicks, pipe-cleaners, etc. Extensions/Variations: There are a lot of different ways to approach this lab depending on what you want your students to learn from it and how well they understand the material going into the activity. • Add or subtract chromosomes • Change mode of inheritance/phenotypes • Model recombination, mutation, or nondisjunction
  20. 20. Marshmallow Meiosis – Handout Name: Date: For Teacher – answers in bold A new species called Reebops has recently been identified in the area. Not much is known about these unique animals; however genetic analyses have revealed that Reebops (2n=16) are a diploid species just like humans (2n=46). How many chromosomes are in a Reebop somatic cell? 16 How many chromosomes are in a Reebop gametic cell? 8 We have been fortunate enough to capture two Reebops; a male and a female. Both the male and the female have been determined to be heterozygous at all loci. What does “heterozygous at all loci” mean? Two dissimilar alleles coding for every gene in a genotype There has been quite a bit of success in mapping the Reebop chromosomes. In fact an observable phenotypic characteristic has been mapped to each of the chromosomes. A chart revealing the phenotype of the genetic code is attached. This will make it possible to visualize possible progeny of the Reebops we have captured. The Reebop has eight pairs of chromosomes. How many chromosome combinations are possible from an organism that has eight pairs of chromosomes? 2^8
  21. 21. You have been given a representation of both the female and male Reebop chromosome sets. It is your mission to create gametes through simulation of meiosis and determine the phenotype of the baby Reebop you have developed. The Reebop chromosomes have been numbered from 1 to 8 from longest to shortest. Record the allele(s) you have in your gamete for both your female and male. 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8 When these two gametes are combined via fertilization what is the resulting genotype of the progeny created? Using the phenotype coding chart provided what is the phenotype of your baby Reebop? Chromosome Genotype Phenotype 1 2 3 4 5 6 7 8
  22. 22. 1 AA 1 antenna 1 Aa 2 antenna Incomplete Dominance 1 aa No antenna 2 MM 1 green hump 2 Mm 2 green humps Incomplete Dominance 2 mm 3 green humps 3 QQ Red nose 3 Qq Orange nose Incomplete Dominance 3 qq Yellow nose 4 TT or Tt Curly tail Complete Dominance 4 tt Straight tail 5 EE or Ee 2 eyes Complete Dominance 5 ee 3 eyes 6 LL or Ll Blue legs Complete Dominance 6 ll Red legs 7 DD or Dd 3 body segments Complete Dominance 7 dd 2 body segments 8 XY Male Incomplete Dominance 8 XX Female
  23. 23. Handout Stages of Meiosis http://www.bbc.co.uk/schools/gcsebitesize/biology/cellprocesses/celldivisionrev3.shtml
  24. 24. Lesson 5 Transcription and Translation DNA to Protein Objective: Simulate the processes of transcription and translation using the provided materials. Grade Level: 9-12 National Standards: • Students should develop an understanding of reproduction and heredity • Students should develop understanding of molecular basis of heredity Background Knowledge: Organisms use DNA as there permanent source of “knowledge” for functioning throughout their lives. As cells grow and their environment changes different genes may need to be “turned on” in response to a stimulus. Turning on a gene begins the process of transcription and translation to make functional proteins that help the organism to survive and/or react to their surroundings. This is a complicated process however, this activity is designed to create a balance by displaying most of the intricacies of the process but also simplifying it to a level the students can understand. For this activity, we will use Velcro as the DNA and RNA and paper clips for the amino acids. Vocabulary: • Transcription: the process of transcribing DNA to messenger RNA • Translation: the process of translating messenger RNA to protein (amino acids). • 5’ end: end of DNA on which transcription ends and end of RNA which translation begins. • 3’ end: end of DNA on which transcription begins and end of RNA which translation ends. • Codon: three letter code on the messenger RNA that codes for an amino acid • Anti-codon: three letter code on the transfer RNA that matches a codon on the messenger RNA • Coding region: a portion of DNA (or messenger RNA) that contains a sequence that codes for a protein
  25. 25. • Initiation codon: a codon (AUG) that begins the translation process from messenger RNA to protein • Termination codon: a codon (UAA or UAG) that stops the translation process from messenger RNA to protein • Point mutation: a single nucleotide change (e.g. from A to T) • Frame shift: when the ribosome shifts over and begins reading in a different frame (from reading AUG CGA ATT to reading UGC GAA TT) Materials: • Velcro – chromosomes nucleotides anticodons • Duct tape (to attach nucleotides to each other) • Paper clips (amino acids) – 20 different colors (How many amino acids are there?) • Reference Materials Procedures: 1. Carefully read through these instructions and check off each step as you go. 2. Discuss in your group how transcription and translation occur; think about all of the organelles and components that are necessary for transcription and translation to occur (your vocabulary list on the first page may be a good starting point… but not a complete list). Jot down the ideas your group forms. 3. Write-up a procedure that you will use to simulate the processes. Try to be as specific as possible about all steps involved and describe them in detail in your write-up. Be sure to assign each group member a role in the process and record their role as part of your procedure write-up. 4. Important things to remember include: What are the start sequences? What are the stop sequences? Which direction does transcription occur? Which direction does translation occur? Where in the cell does each activity occur? 5. Practice transcription and translation using the procedure your group has worked out. 6. Answer these questions (as a group) and include in your final write-up: a. How do the activities, transcription and translation (that a cell carries out), relate to the mapping, sequencing, and understanding of genomes? b. Mutations can be very detrimental to an organism. What checks do transcription and translation have to attempt to prevent these detrimental mutations from occurring? 7. If time permits we will exchange procedures to compare how other groups approached the processes. Assignment: Complete the above activity and have one group member type your procedure including steps 2, 3, 4, and 5.
  26. 26. As the codon As the anti-codon CCC Proline Glycine CCU Proline Glycine CCA Proline Glycine CCG Proline Glycine CUC Leucine Aspartic Acid CUU Leucine Aspartic Acid CUA Leucine Glutamic Acid CUG Leucine Glutamic Acid CAC Histidine Valine CAU Histidine Valine CAA Glutamine Valine CAG Glutamine Valine CGC Arginine Alanine CGU Arginine Alanine CGA Arginine Alanine CGG Arginine Alanine ACC Threonine Tryptophan ACU Threonine None ACA Threonine Cysteine ACG Threonine Cysteine AUC Isoleucine None AUU Isoleucine None AUA Isoleucine Tyrosine AUG Methionine (initiation) Tyrosine AAC Asparagine Leucine AAU Asparagine Leucine AAA Lysine Phenylalanine AAG Lysine Phenylalanine AGC Serine Serine AGU Serine Serine AGA Arginine Serine AGG Arginine Serine UCC Serine Arginine UCU Serine Arginine UCA Serine Serine UCG Serine Serine UUC Phenylalanine Lysine UUU Phenylalanine Lysine UUA Leucine Asparagine UUG Leucine Asparagine UAC Tyrosine Methionine UAU Tyrosine Isoleucine UAA Stop Isoleucine UAG Stop Isoleucine UGC Cysteine Threonine UGU Cysteine Threonine UGA Stop Threonine UGG Tryptophan Threonine GCC Alanine Arginine GCU Alanine Arginine GCA Alanine Arginine GCG Alanine Arginine GUC Valine Glutamine GUU Valine Glutamine GUA Valine Histidine GUG Valine Histidine GAC Aspartic Acid Leucine GAU Aspartic Acid Leucine GAA Glutamic Acid Leucine GAG Glutamic Acid Leucine GGC Glycine Proline GGU Glycine Proline GGA Glycine Proline GGG Glycine Proline NSF GK-12 Rural Science Education Program, Oregon State University http://cropandsoil.oregonstate.edu/gk12
  27. 27. From: http://www-stat.stanford.edu/~susan/courses/s166/node2.html NSF GK-12 Rural Science Education Program, Oregon State University http://cropandsoil.oregonstate.edu/gk12
  28. 28. http://allserv.rug.ac.be/~avierstr/principles/pcr.html NSF GK-12 Rural Science Education Program, Oregon State University http://cropandsoil.oregonstate.edu/gk12
  29. 29. Lesson 6 Animal Genetics Objective: • Students will understand how Punnett Squares work. • Students will understand the relationship between genotypes and phenotypes. • Students will explore how limited alleles produce genetic diversity. Grade Level: 6-12 National Standards: • Students should develop an understanding of reproduction and heredity • Students should develop understanding of molecular basis of heredity Background Knowledge: Students should be familiar with Genotypes and Phenotypes and have some notion of heredity. Materials Needed: • Dice • Marker/Crayons • Animal Genetics Worksheets Vocabulary: • Allele – one form of a gene. • Loci – location of a gene on the chromosome. • Diploid – having two copies of each chromosome, therefore having two alleles for each gene. • Genotype – set of alleles for a given gene. If diploid, 2 letters Tt, aa, etc. • Phenotype – expressed (visual) form of the gene. Tall plant, Purple skin, O blood type, etc. • Polymorphism – a gene having more than two common phenotypes. Red, pink, and white. • Homozygous – having two identical alleles for a specific loci. Can be either homozygous dominant (AA) or homozygous recessive (aa). • Heterozygous – have two different alleles for a specific loci (Aa). • Hybrid – same as heterozygous. • Complete dominance – dominant allele is always expressed and recessive phenotype will only be expressed if homozygous recessive. TT or Tt = tall and tt = short.
  30. 30. • Incomplete dominance – both alleles are responsible for resulting phenotype. RR = red, Rr = pink, rr = white. • Punnett Square – this is used for predicting crosses for a specific trait. • Multiple loci phenotypes – traits in which several different loci are responsible for the phenotype. • P generation – parental generation, • F1 generation – first filial generation (first cross). • F2 generation – second filial generation (second cross). Procedure: This series of activities have been created to help students master using a Punnett Square. 1. In Advance: Draw the Parent Animals based on the Punnett Squares on the worksheet (Mom is across the top, Dad is on the left) 2. Model completing the first Punnett Square on the board or an overhead. Complete the square, identify which square is being used (based on a roll of the dice) and figure out the genotype and phenotype. 3. Give each student a die (they will have to share for the dihybrid crosses if you are doing cows or horses). Have the students roll the die one time and stop. If they have rolled between a 1 and 4, have them write their number in the blank for dice roll for the first trait. If they rolled a 5 or a 6 they need to roll again until they get between 1 and 4. Have the students do all their dice rolling at once so that you can collect the dice and no more noise. 4. Have students complete the Punnett Squares. 5. Have students draw a picture of the animal their worksheet produced. (For students who do not like to draw having a blank outline for them to use helps.) 6. Display all the drawings. This is the first generation from one set of parents. The class can make observations about the frequency of traits and diversity, recessive and dominant traits can be discussed. Extensions: • Have the kids proceed through and make a second generation. • Comparison of theoretical and actual phenotypic ratios can be calculated. • Other questions can be asked to get the students to think about how the information can be used for agricultural and scientific reasons.
  31. 31. Sample Student Worksheet- Cats Name: ______________________ Fill in the missing information for each trait. After you have determined all the traits your kitten will have, make a drawing of your cat. Name your cat and write a description of your cat that includes all of the phenotypes it received from its parents. Complete Dominance Traits Trait #1: Stripes White stripes (W) is the dominant trait. No stripes (w) is the recessive trait. Parent #1 is a hybrid with white stripes (Ww) and parent #2 has no stripes (ww). w w Genotype Phenotype 1 2 Dice roll = ______ WW White Kitten genotype = ______ W stripes Ww White 3 4 Kitten phenotype = stripes w ww No stripes ____________________ Trait #2: Tail length Normal tail (N) is the dominant trait. Bobbed tail (n) is the recessive trait. Parent #1 is a hybrid with normal tail (Nn) and parent #2 has a bobbed tail (nn). n n Genotype Phenotype 1 2 Dice roll = ______ NN Kitten genotype = ______ N Nn 3 4 Kitten phenotype = n nn ____________________ Trait #3: Ear shape Pointed ears (P) is the dominant trait. Rounded ears (p) is the recessive trait. Parent #1 is a hybrid with pointed ears and parent #2 is a hybrid with pointed ears. Genotype Phenotype Dice roll = ______ 1 2 Kitten genotype = ______ Kitten phenotype = 3 4 ____________________ Trait #4: Gender The father is male (XY). The mother is female (XX). Genotype Phenotype Dice roll = ______ 1 2 Kitten genotype = ______ Kitten phenotype = 3 4 ____________________ NSF GK-12 Rural Science Education Program, Oregon State University http://cropandsoil.oregonstate.edu/gk12
  32. 32. Incomplete Dominance Traits Trait #5: Nose Color In this case, each genotype produces a different phenotype since the dominance is incomplete. Both parents have a spotted nose. Genotype Phenotype 1 2 Dice roll = ______ BB Black Kitten genotype = ______ Bb Spotted 3 4 Kitten phenotype = bb Pink ____________________ Trait #6: Fur length In this case, each genotype produces a different phenotype since the dominance is incomplete. Both parents have medium length fur. Genotype Phenotype 1 2 Dice roll = ______ LL Long fur Kitten genotype = ______ Ll Medium 3 4 Kitten phenotype = fur ll Short fur ____________________ Trait #7: Eye color In this case, each genotype produces a different phenotype since the dominance is incomplete. Both parents have green eyes. Genotype Phenotype 1 2 Dice roll = ______ BB Brown Kitten genotype = ______ Bb Green 3 4 Kitten phenotype = bb Blue ____________________ Co-dominant trait with 2 genes Trait #8: Fur color In this case, each genotype produces a different phenotype since the dominance is incomplete. Both parents have brown fur. Gene #1 is F and Gene #2 is P. Genotype Phenotype Gene #1 Gene #2 FFPP Pink FFPp Tan 1 2 1 2 FFpp Blue FfPP Black FfPp Brown 3 4 3 4 Ffpp Orange ffPP Green ffPp Gray Dice roll = ______ & ______ Kitten genotype = ______ ffpp Purple Kitten phenotype = ___________ NSF GK-12 Rural Science Education Program, Oregon State University http://cropandsoil.oregonstate.edu/gk12
  33. 33. Lesson 7 Fruit Fly Ranching … Student Outcomes/Objectives • to gain a better understanding of genetics and its application to a particular organism (in this case Drosophila – the common fruit fly) • to gain a better understanding of the Punnett Square and applying this knowledge to find combinations of desirable traits • to become familiar with and gain experience in running a business • to be exposed to the idea of business proposals, loan approval forms, business ledgers, using checks, and dealing with income taxes National Standards: • Students should develop an understanding of reproduction and heredity • Students should develop understanding of molecular basis of heredity Background Knowledge: This lesson plan combines both science and business to form a fun and active classroom project. This lesson plan is an excellent way for students to take what they learn in the classroom and apply it to the real world. Material • Drosophila • Plastic Vials w/ foam stoppers • Growing Medium • Q-Tips • Fly Nap • Ledger Forms • Loan Approval Forms • Check Forms • Masking Tape • Grease Pencil/Marker • Candy/Prizes • Price Sheet Forms • Magnifying Glass Worksheets Fruit Fly Ranch Loan Paperwork My Fruit Fly Ranch Example Result Form Teacher Keys *Italicized words in lesson plan are potential script for teacher (add this if teacher scrip is included in lesson plan)
  34. 34. Fruit Fly Ranching Fruit Fly Ranch Activity Procedures 1. This is a culminating inquiry-based activity that follows a discussion of the basics of genetics. The students should be familiar with the terms Genetics, Heredity, Traits, Genotype, Phenotype, Punnett Squares, Generations, Offspring, Monohybrid, Dihybrid, and Genotypic/Phenotypic Ratios. The students should also be familiar with the traits of Drosophila. 2. After our discussion of genetics, the students are shown a number of vials containing Drosophila. The students are then asked what traits the flies have in common and some traits that are different. After the students have composed the list, each student is given a price sheet of the value of certain combinations of traits. 3. Without instruction or guidance the students are then assigned to raise fruit flies on their own ranch in order to earn as much money they can by selling the flies that they have raised. However before the student may begin, each student must submit a one-page “Business Proposal” to the bank in order to borrow money to get his or her business started. The proposal should include the name of the ranch, materials needed, the purpose of the loan, what parents will be used, what is the expected outcome, a timeline of anticipated events and a schedule of payback for their loan. Also have the students budget a little extra money in case of unforeseen expenses. 4. Once a proposal has been approved, the student is asked to sign a contract with the bank and checks are issued (Loan Approval Form). It is also necessary to discuss with the students what checks are used for, how they work and how a check is filled out. It is a good idea to have the students practice writing the checks at this time. 5. Another item that is given to the student is a business ledger. This is used to track the income and expenses of the ranch. Again this it is vital to discuss the differences between income and expenses and have the students practice keeping track of these items using the Ledger Forms. Each student is required to keep a running balance of the money in their accounts and each has a file folder with their names on them. Be sure and occasionally check their balances with the banks balances to make sure they don’t bounce checks. If a student bounces a check, normal bank fees apply. This may mean that the student will have to borrow more money. 6. It is time for the students to begin raising their flies. The students need to purchase their supplies and materials (using checks) and create a home for their flies. Be sure that instructions for preparation of growing medium are given.
  35. 35. 7. After the growing medium has been prepared, the students will now wait for their flies to grow. Every couple of days the students are required to check on their vials and note changes that occur within. 8. Once the flies have matured and emerge, the flies will be put to sleep using the fly nap and q-tip. The students will then use a magnifying glass to separate the flies with the different traits, i.e. eye color, wing shape and to count the number of each. The flies will then be counted and assigned a value by the teacher and this will give the students their gross income. 9. After the students have found out how much money they have earned, they are then asked to repay the balances of their loans. Finally the idea of income taxes is introduced. Depending on the amount that they student earned, they are assigned a tax bracket and are asked to write a check to state and federal agencies for their taxes. This will give us the student’s disposable income. This is the amount that the students are allowed to spend for prizes following the activity. Prizes can include candy, toys, classroom supplies, periodic tables, hall passes, homework passes, etc. Assessment There are a variety of ways to assess the students for this activity. Ideas are counseling peers on how to make more money, rewriting their business proposal so that they could make more money if the activity were repeated, posters of their experiments and results or merely having the students write what they have learned from the activity.
  36. 36. Fruit Fly Ranch Loan Paperwork Date: _______ Regarding: Loan for (Ranch Name) Dear Mr. / Ms. (Student Name) This letter is to inform you that your loan has been granted. We look forward to seeing your business venture grow and be very successful. We are here to assist you in any way possible. Please note that you must pay us back in a timely manner. Your total loan must be paid back after your 5th payment. Please see below for your loan costs. Loan Amount $ 445.00 Interest (10%) $ 44.50 Payment Amt $ 61.19 Balance due after 5th Payment $ 183.56 I have read and understand the terms of the above agreement. I promise to make all payments on time, if I do not pay on time I could be charged a late fee. Signed: _________________________________________ __________________________ Rancher Bank Manager
  37. 37. Name ___________________ My Fruit Fly Ranch Date Activity Income Expenses Balance Opening Balance $ 400.00 $ 400.00
  38. 38. Example Result Form Tax Tax Net Rate Amount Total Gross Less Loan Payment Amount Dustin $1,210 0 $0 $1,210 $ 647.62 $562 Michael $2,045 0.1 $205 $1,841 $ 435.00 $1,405.50 Lindsey $2,255 0.1 $226 $2,030 $ 330.00 $1,699.50 Andi $2,315 0.25 $579 $1,736 $ 428.31 $1,307.94 Yessenia $2,770 0.25 $693 $2,078 $ 302.04 $1,775.46 Ben $3,920 0.35 $1,372 $2,548 $ 529.24 $2,018.76 Zack $3,630 0.35 $1,271 $2,360 $ 369.60 $1,989.90 Naomi $4,100 0.4 $1,640 $2,460 $ 301.24 $2,158.76 Julia $4,755 0.4 $1,902 $2,853 $ 395.00 $2,458.00 Michael $9,230 0.45 $4,154 $5,077 $ 1,052.70 $4,023.80 Jarred $16,282 0.45 $7,327 $8,955 $ 690.62 $8,264.48
  39. 39. Lesson 8 DNA Extraction Objective: Students will learn how to extract DNA from living sources using household reagents National Standards: • Students should develop an understanding of reproduction and heredity • Students should develop understanding of molecular basis of heredity Background knowledge: Students should have a general knowledge of what DNA is and cell structure. Materials needed: • DNA sources (wheat germ, apple, onion, kiwi, potato, beef liver) • Soap (liquid dish soap) • Salt • Enzyme (meat tenderizer) • Room temperature water • Alcohol (97% EtOH) • Plastic test tubes with caps • Knife to cut DNA sources • Mortar and pestle (to macerate samples) • Gauze • Funnel • Small beaker (to transfer EtOH in to test tubes) • Disposable plastic pipettes (to dispense soap) • Wooden skewers Procedure: It is best if you can have small chunks of DNA sources cut up for the students and kits with everything they need set out at their lab stations. This prevents a lot of chaos and “lost” reagents during the lab. Either provide the students with a set of directions or have them write the procedure up themselves. Be sure to discuss what role soap, meat tenderizer, and alcohol may play in the extraction. 1. Macerate your DNA source with a mortar and pestle.
  40. 40. 2. Mix macerated sample with a pinch of salt and tap water (2x the volume of the sample) to create a “cell soup”. 3. Strain the soup using gauze in a funnel into a test tube. The test tube should be half-full at maximum. Discard anything more than half of the test tube volume. 4. Add detergent (~1/6 the volume of the strained soup volume). Replace tube cap and swirl gently or gently invert the tube to mix. Try to create as few bubbles as possible. Let this mixture set for 7-10 minutes. 5. Add a pinch of enzyme (meat tenderizer) to test tube; swirl gently – being too rough will break DNA making it difficult to see. 6. Tilt the test tube and slowly add an equal volume of iced EtOH. 7. Tilt the test tube back upright and watch for a layer of DNA to form (between water and alcohol layers). 8. Use a wooden skewer or glass rod to hook the DNA into the alcohol and cause further precipitation. Extensions/Variations: Many extensions and variations can be done with this lab. 1. Provide both living and nonliving sources and see what you can extract DNA with. 2. Try different reagents (different soaps, different enzyme sources like pineapple juice or contact solution, etc.) and see if you can achieve the same results. Additional lesson: DNA Jewelry – Resource: http://www.fresno.k12.ca.us/schools/S090/_atkinsgatebio/beadproject/GenJewelProjCtr.html
  41. 41. Name____________________________ Date_____________________________ What do you already know What do you want to know What have you learned about DNA? about DNA? about DNA? 1. Where is DNA found? 2. Do all living things have DNA? 3. Who first proposed the double helix structure of DNA and when did they do it? 4. DNA is composed of nucleotides. What is a nucleotide? 5. The base pairing rules are very important in DNA replication. a. What are the 4 bases in the DNA molecule? b. What bases pair together?
  42. 42. c. How does this help DNA replicate? 6. What is the difference between DNA and RNA? 7. What is a chromosome? 8. What is a histone? What would happen if no histone was present? 9. ____________ occur when changes in genetic information occur due to alteration in the DNA sequence. 10. Complete the polypeptide sequence based on the DNA sequence: ATGATTCCTGTGGGT 11. Draw and label a DNA molecule. 12. How can polyploidy in plants benefit humans?
  43. 43. Teacher Copy Name____________________________ Date_____________________________ What do you already know What do you want to know What have you learned about DNA? about DNA? about DNA? 1. Where is DNA found? In all living things 2. Do all living things have DNA? YES 3. Who first proposed the double helix structure of DNA and when did they do it? Watson and Crick; 1953 4. DNA is composed of nucleotides. What is a nucleotide? A phosphate molecule attached to a sugar molecule; these molecules are linked together to for a DNA or RNA strand; aka A, G, C, and T in DNA or A, G, C, and U in RNA. 5. The base pairing rules are very important in DNA replication. a. What are the 4 bases in the DNA molecule? Adenine (A), Guanine (G), Thymine (T), Cytosine (C) b. What bases pair together? A-G C-T
  44. 44. c. How does this help DNA replicate? Unwound strands of DNA reveal a single strand of nucleotides which serve as a template for new DNA 6. What is the difference between DNA and RNA? i. Both DNA and RNA consist of a long chain of nucleotides ii. DNA contains the base thymine (T), not uracil (U) iii. RNA contains the base U, not T 7. What is a chromosome? Structure which contains genetic factors as DNA (or RNA) arranged in linear order 8. What is a histone? What would happen if no histone was present? The protein DNA wraps around in eukaryotic chromosomes; No double helical structure 9. ___Mutations___ occur when changes in genetic information occur due to alteration in the DNA sequence. 10. Complete the polypeptide sequence based on the DNA sequence: ATGATTCCTGTGGGT Met – Ile – Pro – Val – Gly ___ 11. Draw and label a DNA molecule. 12. How can polyploidy in plants benefit humans? - Improved yields - Seedless fruits
  45. 45. Lesson 9 Gel Electrophoresis Protocol for Pouring, Loading, and Running a DNA Agarose Gel Objective: Students will learn how to pour load and run an agarose gel National Standards: • Students should develop an understanding of reproduction and heredity • Students should develop understanding of molecular basis of heredity Pouring a Gel Materials • 0.45 g Agarose • 45 ml 1 x TBE • Gel Tray • Lab tape • Plastic wrap • Well comb Procedure 1. Tape sides of gel try to prevent Agarose from leaking 2. Make sure tray is on a level surface 3. Add measured Agarose powder to a flask 4. Add measured 1 x TBE to flask 5. Swirl to mix 6. Cover with plastic wrap. Poke holes in plastic wrap with a pipette tip (to allow steam to escape, but prevent loss of liquid) 7. Heat on a hot plate until Agarose is dissolved (~ 12 min on high) 8. Swirl solution occasionally during heating 9. Let solution cool until you can touch it 10. Pour into prepared gel tray with comb in place
  46. 46. 11. Check for bubbles and use a pipette tip to pop any found 12. Let solidify (~30 minutes depending on the size of the gel) 13. If not using your gel immediately, store at RT in 1X TBE solution
  47. 47. Loading a Gel Materials • Solidified Gel • Electrophoresis • 1X TBE • DNA Samples • Standard Procedures: 1. Place the tray with the solidified gel into the electrophoresis box 2. Make sure the whole gel is just covered with 1x TBE 3. Carefully, remove the comb while holding the tray in place 4. Load the measured amount of sample into the well and brace your hand if necessary ∗ Depending on the size of the well load 5-15 μL total volume. The sample should include loading dye. Loading dye is made mostly of sucrose and a dye. The sucrose weighs down the DNA sample so it drops to the bottom of the gel well and the dye allows for visualizing how far the samples have traveled down the gel. Depending on the size of the sample add between 1-3 μL of loading dye. ∗ Loading dye has been added to some samples during the extraction procedure. Some samples may require you to add dye to samples before loading in the gel.
  48. 48. Running a Gel 1. Place the top of the electrophoresis unit onto the box making sure that the contacts are appropriately connected (black to black, red to red) ∗ Have the negative electrode at the well end of the gel. DNA is negatively charged. Opposites attract and likes repel so with negative DNA at the negative electrode the DNA will travel away from the negative current and toward the positive current. 2. Plug the unit into the power source (again: black to black, red to red) 3. Turn unit on, set to desired voltage, begin run 4. Run ~ 20 min @ 200V or 40 min @ 100V; you can determine how far the gel has run by the distance the loading dye has gone. 5. Turn power unit off before disconnecting the apparatus. Alternative Staining Procedure using Methylene Blue ∗ This procedure is non-hazardous and you can visualize the fragments on a simple light box. Limitations of the methylene blue technique are: less sensitivity (requires more DNA) and requires a longer staining and destaining times to visualize the DNA fragments 1. 0.025% Methylene Blue Procedure a. Flood gel with 0.025% methylene blue (dilute 0.1% methelyne blue 50μL with ddH2O (200mL)), stain 20-30 minutes or continue staining overnight at 4C. b. The next day place the stained gel in clean water and rinse until gel is destained; Let gel soak for several minutes in several changes of fresh water. DNA bands
  49. 49. will become increasingly distinct as gel destains. You may continue to destain overnight in a small volume of water if necessary. (Gel may destain too much if left overnight in large volume of water.) c. Cover staining tray to retard evaporation. d. View gel over light box; cover surface with plastic wrap to prevent staining. 2. 0.1% Methylene Blue Procedure a. Coat gel in 0.1% methylene blue, let stain one minute b. Destain gel in successive water washes c. You may continue to destain overnight in a small volume of water if necessary. (Gel may destain too much if left overnight in large volume of water.) d. Cover staining tray to retard evaporation. e. View gel over light box; cover surface with plastic wrap to prevent staining.
  50. 50. Figure from: http://en2.wikipedia.org/wiki/Agarose_gel_electrophoresis (1) The agarose gel with three slots (S). (2) Injection of DNA ladder into the first slot. (3) DNA ladder injected. Injection of samples into the second and third slot. (4) A current is applied. The DNA moves toward the positive anode due to the negative charges on its phosphate backbone. (5) Small DNA strands move fast, large DNA strands move slowly through the gel. The DNA is not normally visible during this process, so the marker dye is added to the DNA to avoid the DNA being run entirely off the gel. The marker dye has a low molecular weight, and migrates faster than the DNA, so as long as the marker has not run past the end of the gel, the DNA will still be in the gel. (6) The DNA is spread over the whole gel. The electrophoresis process is finished.

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