Cathryn Kurkjian, PhD Postdoctoral Trainee University of North Carolina, Chapel Hill.

Transcription

1 [Type here] [Type here] [Type here], PhD Postdoctoral Trainee University of North Carolina, Chapel Hill Image from:

2 Contents Grade Levels... 2 Subject Area... 2 Objectives... 2 Method... 2 Materials... 2 Duration... 2 Group Size... 2 Key Words... 3 Background... 3 Procedure... 4 Flip the classroom!... 4 Engage... 4 Explore... 4 Explain... 5 Elaborate... 6 Evaluate... 6 Resources... 7 Standards... 7 NC essential Standards... 7 Common Core (grades 9-10)... 7 Common Core (grades 11-12)... 7 Next Generation Science Standards... 8 Amino Acids sheet (cut-outs for activity)... 9 DNA sequence sheet (cut-out for activity Student Handout

3 Grade levels: High school (9-12) Subject areas: Biology Objective: Practice note taking skills and engage in active learning Describe various molecules found within cells (i.e. DNA, RNA, genes, proteins, amino acids) Explain DNA transcription and translation through constructing a protein sequence from a given DNA sequence Interpret results and use this knowledge to hypothesize how defects in transcription and translation can result in disease Method: Teachers should flip the classroom, having students complete a homework assignment prior to the classroom activity. Students will complete an activity that demonstrates how DNA transcription and translation occurs within mammalian cells. Following the engaged learning activity, the instructor will present a lecture that gives in depth information on transcription and translation to build on the concepts students learned during the activity. By the end of the lesson, students should be able to discuss DNA transcription and translation, construct a protein from a given DNA sequence, and apply this knowledge to understanding how there may be disease states related in transcription and translation misregulation. Materials: Handout Informational sheet for activity (1) plastic Easter egg or (1) small Tupperware container to serve as the cell nucleus Construction paper cut into a long strip, labeled with a DNA sequence and folded to place inside the nucleus Construction paper cut-outs with amino acid 1-letter abbreviations Ziploc bags (sandwich or snack size) to store amino acids (1 bag per group) Glue sticks or Scotch tape Optional: The Biology Coloring Book by Robert D. Griffin Optional: YouTube video ( and appropriate technology for watching the video Duration: Approximately two 50 minute class periods Group Size: This lesson plan is appropriate for all class sizes. For the activity, students should work in groups of

4 Key Words: Deoxyribonucleic acid (DNA) Encodes your genetic information Genome An organisms complete set of DNA Genes Made of DNA, genes act as instructions for making proteins; the human genome contains about 30,000 genes Nucleotide bases (nucleobases) Forms basic structural unit of DNA and RNA Purines: Adenine and Guanine Pyrimidines: Thymine, Cytosine, and Uracil (note: in RNA, Uracil replaces Thymine) Nucleotide pairing Also known as base pairing, is the joining of purine to a pyrimidine through a hydrogen bond link (A T, C G, or A U in RNA) Ribonucleic acid (RNA) Messenger to carry instructions from DNA for controlling protein synthesis messenger RNA (mrna) Synthesized from DNA during transcription, mediates transfer of genetic information from the nucleus to the cytoplasm transfer RNA (trna) RNA molecules that carry amino acids to ribosome to form polypeptides ribosomal RNA (rrna) Assembles amino acids into polypeptides that make up proteins Amino Acids An organic compound composed of a carboxyl group and an amino group; the building blocks of proteins Polypeptides Polymer consisting of a number of amino acids Protein Molecule made of one or more long chains of amino acids Ribosome A large complex of proteins that acts as the machinery involved in translation; complex containing RNA and proteins Sequence hypothesis Initially proposed by Francis Crick in 1958, this hypothesis states that the DNA sequence codes for the amino acid sequence Transcription The process of making an mrna sequence from a gene sequence (DNA) template Translation The process of translating mrna into a strand of amino acids (protein) Background: Deoxyribonucleic acid, or DNA, encodes for our entire genetic information. Nucleotide bases, or nucleobases, are the building blocks of DNA. While there are only 4 distinct nucleobases used to construct DNA, the human DNA is made up of a total of about 3 billion bases! The organization of these bases is what determines how things are made in the human body. The sequence of DNA within an individual is like a very large book, and every single person has a unique sequence that sets them apart. Our genome, or our complete set of DNA, is located within the nucleus of all the cells within our body. Important properties of DNA include its ability to replicate during cell division and its ability to drive protein synthesis. However, DNA must perform these functions while never leaving the nucleus. The nucleus is like a vault in a high security bank. While there are certain molecules that are able to enter and exit, DNA must remain within the nucleus at all times under strict guard. DNA, therefore, must utilize various mechanisms to complete its work from within the confines of the nucleus. Proteins are the building blocks of all the tissues in our body; additionally, protein aids in tissue repair and makes up the various chemicals within our bodies (i.e. hormones and enzymes). Genes are regions of DNA that act as templates making proteins through a process known as protein synthesis. DNA must therefore have a mechanism to get the genetic information copied and made into proteins. These processes are what we refer to as transcription and translation. Transcription is the process in which RNA copies the genetic sequence. This copied sequence, or mrna, is able to leave the nucleus where it can then direct protein synthesis. Translation is the process in which the mrna sequence is decoded into a sequence of amino acids. The ribosome, which is located within the cytoplasm, is the machinery that can read the mrna sequence and stitch amino acids together to generate a protein that has a specific function. 3

5 Procedure: Flip the classroom! 1. A homework assignment that describes the process of DNA transcription and translation should be provided prior to this lesson plan. This will allow students to have a brief understanding of the lesson prior to coming to class. a. Example: The Biology Coloring Book by Robert D. Griffin i. This book contains information and coloring exercises for various cell biology topics, including DNA transcription and translation. In addition to giving a brief introduction to the topic, it also requires that students color in the various components of the processes as a mechanism for learning the new material. Engage 2. Start the class off by asking students what they know about proteins based on their previous knowledge of cells, DNA and the human body. a. Think-Pair-Share: Ask students to take about 30 seconds to come up with ideas, and then take another minute to discuss these ideas with their neighbor. b. List and Record: Call on individuals to share their responses. Compile a list on the board of these responses and engage students in a discussion. i. What do they already know about proteins? What questions do they have? 3. Background information a. If using an introductory homework assignment prior to class, discuss the highlights from the assignment at this time. i. What are some key differences between DNA and RNA ii. What are nucleotides? How does nucleotide pairing work? iii. How do you get from DNA RNA proteins? Explore 4. Transcription and Translation Activity a. Illustrate how transcription and translation work through an example. i. A good example to introduce these concepts is the Rosetta Stone The Rosetta Stone is a very important part of Egyptian history. It is a large black granite stone bearing three inscriptions: (1) ancient Egyptian hieroglyphs, (2) Egyptian demonic script and (3) Ancient Greek. It is considered the key to modern understanding of Egyptian hieroglyphs since it contained the same passage in these three different languages. Issued at Memphis, Egypt in 196BC on behalf of King Ptolemy V. It is believed to have been created following the coronation of King Ptolemy V, and the decree established the divine cult of the king. It is believed to be housed at various locations, but is now located at the British Museum (1802) where it is on display to the public. But what does this have to do with transcription and translation?! 1. We want to know what the script says. We cannot take the stone away from the British museum because it is too big (over 1,000lb!) and because it is against the law! So how do we go about trying to figure out what is written on the stone? 2. First, we must go to the British Museum and Transcribe, or copy, the text onto a piece of paper that we can carry with us. 4

6 3. However, we cannot read any of these ancient texts! So what do we do next? 4. We must take the paper containing the transcribed text and bring it to translators outside of the museum who are able to read the language and translate it to English. ii. The process of turning DNA into protein is very similar to this. DNA is found within the nucleus of a cell. It must stay within the nucleus, so we must go there to transcribe it. The transcribed material (mrna) is then able to leave the nucleus and be translated into amino acids which make up a protein. Let s see if we can understand the process through doing this activity. iii. Knowing that information, you can go back and ask the questions: 1. What does the museum represent? Nucleus 2. What does the individual transcribing the text represent? Transcription 3. What does the translator represent? Translation; the Ribosome b. Have students form groups of 2-4 students. c. All students will receive a handout containing a chart showing how to transcribe DNA to RNA and how to translate RNA to protein. This handout will also bare the question, Who s hungry?. The results from this activity will give the answer, PACMAN AND HIS WIFE! d. At the front of the room, the students can find the nucleus (a plastic Easter egg or a small Tupperware container) that contains the genomic information (a DNA sequence written on a piece of construction paper) that we want to use to make protein. e. Students must go to the front of the room and, using their worksheet as a guide, transcribe the DNA into RNA. Once it is transcribed, they can return to their seats to translate the sequence. f. The students will have various pieces of construction paper containing the one letter abbreviations of various amino acids. They will use their handout to determine the amino acid sequence that correlates with their RNA sequence. The amino acids can be glued or taped to their handouts. They have now translated the RNA sequence into a polypeptide. g. If they have correctly gone through the steps of transcription and translation, then the resulting string of 1 letter amino acids while bare the answer to the question. Explain 5. Discuss the results from the activity as a class. Were students about to get the correct answer? If not, determine where the mistakes occurred. a. Was it a transcription error? b. Was it a translation error? 6. Incorporate lecture that gives in depth explanation of how DNA transcription and translation occurs. OR (optional) watch the YouTube video provided above to allow students to get an in depth description of transcription and translation. This video gives detailed explanations of the process beyond the concepts of DNA RNA Protein. After the video, students should have an understanding of the following: a. What are DNA and RNA, and how are they different? b. What are nucleotides? What are the nucleotide pairs for DNA and RNA? c. Where in the cell do transcription and translation occur? d. What are the different types of RNA (mrna, trna and rrna) and what do they do? e. What is an amino acid? How are amino acids processed into a protein (or polypeptide)? 5

7 Elaborate 7. During the explanation following the activity, students should determine if errors occurred at the level of transcription or translation. This can lead to a second class period that focuses on diseases related to defects in transcription and translation. a. The following scientific articles discuss transcription and translation and highlight the various diseases known to be associated with misregulation of these processes. Lee, T.I. and R.A. Young. (2013) Transcriptional Regulation and Its Misregulation in Disease. Cell 152, o Cancer (i.e. breast cancer, prostate cancer, lung cancer) o Autoimmunity and Inflammation o Diabetes mellitus o Cardiovascular disease (congenital birth defects) Scheper, G.C., M.S. van der Knaap, and C.G. Proud. (2007) Translation matters: protein synthesis defects in inherited disease. Nat Rev Gen 8, o Neurodegenerative disease (childhood ataxia with central hypomyelination, CACH) o Wolcott-Rallison syndrome (WRS) o Bone-marrow failure syndrome (i.e. Shwachman-Diamond disease) b. Various lesson plans can be found online demonstrating how point mutations during DNA transcription and translation can result in genetic mutations and disease The Mating Games: Saving Wildlife with Forensic Genetics, the National Math and Science Institute Genetic Mutation worksheet, Lesson Plans inc. ( Genetic Mutations for High School Biology Lesson Plans, Study.com ( c. A potential follow-up assignment could involve students being assigned a disease and doing a report. This report could be a written assignment or a poster that could be presented to the class. Making a poster could be a great group assignment which could allow the instructor to evaluate not only learned material but the ability of students to work in a group environment. Evaluate 8. The initial homework assignment should be graded for completeness. Because it was provided prior to the lesson, it is up to the discretion of the instructor if the assignment should be graded for correct answers. 9. Students should be evaluated for their participation throughout this lesson plan. Participation includes class discussion and working in the groups during the transcription and translation activity. 10. For completion of the activity, students must write down the mrna sequence, construct the amino acid sequence, and determine the answer to the question posed. This handout can be evaluated for completion and correctness. 6

8 Resources: 1. Wikipedia, Rosetta Stone ( 2. YouTube ( 3. The Biology Coloring Book by Robert D. Griffin (1 st edition) 4. Lee, T.I. and R.A. Young. (2013) Transcriptional Regulation and Its Misregulation in Disease. Cell 152, Scheper, G.C., M.S. van der Knaap, and C.G. Proud. (2007) Translation matters: protein synthesis defects in inherited disease. Nat Rev Gen 8, The Mating Games: Saving Wildlife with Forensic Genetics, the National Math and Science Institute 7. Genetic Mutation worksheet, Lesson Plans inc. ( 8. Genetic Mutations for High School Biology Lesson Plans, Study.com ( State and National Standards: North Carolina Essential Standards: Bio.3.1 Explain how traits are determined by the structure and function of DNA. Bio Explain how DNA and RNA code for proteins and determine traits Bio Explain how mutations in DNA that result from interactions with the environment (i.e. radiation and chemicals) or new combinations in existing genes lead to changes in function and phenotype. Bio.4.1 Understand how biological molecules are essential to the survival of living organisms Bio Summarize the relationship among DNA, proteins, and amino acids in carrying out the work of cells and how this is similar in all organisms B.CX.1 Understand the global, historical, societal and cultural contexts of the visual arts B.CX.1.3 Understand how art is used to document human experience.* * Note: This standard is applicable only if using historical text, such as the Rosetta Stone described herein, to introduce the concept of transcription and translation. Common Core (Grades 9-10) CCSS.ELA-LITERACY.RST Follow precisely a complex multistep-procedure when carrying out experiments, taking measurements, or performing technical tasks, attending to special cases or exceptions defined in the text. CCSS.ELA-LITERACY.RST Determine the meaning of symbols, key terms and other domainspecific words and phrases as they are used in a specific scientific or technical context relevant to grades 9-10 texts and topics. CCSS.ELA-LITERACY.RST Compare and contrast findings presented in a text to those from other sources (including their own experiments), nothing when the findings support or contradict previous explanations or accounts. 7

9 Common Core (Grades 11-12) CCSS.ELA-LITERACY.RST Follow precisely a complex multistep procedure when carrying out experiments, taking measurements, or performing technical tasks; analyze the specific results based on explanations in the text. CCSS.ELA-LITERACY.RST Determine the meaning of symbols, key terms and other domainspecific words and phrases as they are used in a specific scientific or technical context relevant to grades texts and topics. CCSS.ELA-LIERACY.RST Synthesize information from a range of sources (e.g. texts, experiments, simulations) into a coherent understanding of a process, phenomenon, or concept, resolving conflicting information when possible. Next Generation Science Standards HS-LS1-1 Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out he essential functions of life through systems of specialized cells HS-LS3-1 Ask questions to clarify relationships about the role of DNA and chromosomes in coding the instructions for characteristic traits passed from parents to offspring 8

10 Print out Amino Acid Blocks on construction paper. Cut blocks out and place into ziplock bag. Each group will get 1 bag containing amino acid blocks from 1 sheet (5 replicates of each AA, 105 blocks total). 9

11 Print out DNA sequence onto Construction paper. Cut out and fold. Insert into a plastic Easter egg or a small Tupperware container. The container will represent the nucleus that the DNA is stored within. 10

12 DNA Transcription and Translation Activity Name Date DNA is made up of nucleotides o Adenine (A) and Guanine (G) are purines o Cytosine (C) and thymine (T) are pyrimidines DNA must form base pairs (or nucleotide pairs) o Purine-Pyrimidine base pairings (A T and C G) result in a proper duplex structure RNA is also made up of nucleotides o Instead of thymine (T), RNA uses uracil (U) o Therefore, A U base pairs occur instead of A T base pairs During Transcription, an RNA sequence is made from DNA o A DNA sequence is: 3 ATG CGC ATG 5 5 TAC GCG TAC 3 You would use the top strand (starting with the 3 ) to make your mrna, so your final result would be: 5 UAC GCG UAC 3 Nucleotides in groups of 3 are translated into amino acids o Using the chart provided, you would determine that the correct amino acid sequence for the above RNA sequence is as follows: Tyr Ala Tyr Amino Acid 3 letter code 1 letter code RNA codons Isoleucine Ile I AUU, AUC, AUA Leucine Leu L CUU, CUC, CUA, CUG, UUA, UUG Valine Val V GUU, GUC, GUA, GUG Phenyalanine Phe F UUU, UUC Methionine Met (start) M AUG Cysteine Cys C UGU, UGC Alanine Ala A GCU, GCC, GCA, GCG Glycine Gly G GGU, GGC, GGA, GGG Proline Pro P CCU, CCC, CCA, CCG Threonine Thr T ACU, ACC, ACA, ACG Serine Ser S UCU, UCG, UCA, UCG, AGU, AGC Tyrosine Tyr Y UAU, UAC Tryptophan Trp W UGG Glutamine Gln Q CAA, CAG Asparagine Asn N AAU, AAC Histidine His H CAU, CAC Glutamic acid Glu E GAA, GAG Aspartic acid Asp D GAU, GAC Lysine Lys K AAA, AAG Arginine Arg R CGU, CGC, CGA, CGG, AGA, AGG Stop codons Stop Stop UAA, UAG, UGA 11

13 Using the information you have previously read and the information provided in this handout, find the answer to the following question: Who s Hungry?! 1. Transcription: Transcribe the DNA found within the nucleus into mrna. 2. Translation: Using the amino acids (1 letter abbreviation) provided, construct the polypeptide (protein). Use scotch tape or a glue stick to adhere the sequence to this handout and determine the answer to the question! 12