Presentation on theme: "Timeline Assignment 1 – DNA Modeling Level: 0 (no experience required) Objective: The student will create structurally accurate models of DNA out of pipe."— Presentation transcript:
1 Timeline Assignment 1 – DNA Modeling Level: 0 (no experience required) Objective: The student will create structurally accurate models of DNA out of pipe cleaners. Materials: pipe cleaners, scissors Tested on: C&I 47330 Curriculum and Instruction in Reading and Writing (Fall 2006) see timeline pictures Assignment 2 – Evolution Models I Level: 1 (basic knowledge of graph theory) Objective: The student will create diagrams of binary evolution trees. Program:graphics package (optional) Tested on: CS10051 Introduction to Computer Science (Spring 2006) Assignment 3 – Evolution Models II Level: 1 (basic knowledge of graph theory) Objective: The student will build on assignment 2 to create diagrams of the incremental k-leaf root evolution model. Program: graphics package (optional) Tested on: CS10051 Introduction to Computer Science (Spring 2006) Assignment 4 – DNA Pattern Statistics Level: 2 (Python programming) Objective: The student will write a program to perform pattern matching statistics on DNA. Program: Python programming language Tested on: CS10061 Introduction to Programming (Spring 2007) Assignment 5 – DNA Visualization Level: 2 (Python programming) Objective: The student will implement and test the chaos-game representation of DNA. Program: Python programming language (with Tkinter graphics library) Tested on: CS10061 Introduction to Programming (Spring 2007) Assignment 6 – Longest Common Subsequence Level: 2 (C++ programming) Objective: The student will implement and test the longest common subsequence dynamic programming algorithm. Program: C++ programming language Tested on: CS33001 Data Structures (Spring 2007) Further Activities Create model of an actual DNA sequence. Longer strands: strands of length 100 can be completed in about two hours, once the procedure is learned and practiced. In groups, use an “assembly line” approach to create a very long DNA strand. Fundraisers (“DNA for a Buck!”) Class contests –create the longest DNA strand –create the strongest DNA strand Step 3: …and do the Twist In “ladder” form, the DNA strand may look inconsistent in size. When twisted into a double-helix form, the inconsistencies tend to work themselves out. N IFTY B IOINFORMATICS A SSIGNMENTS Dean Zeller Department of Computer Science Contact: Dean Zeller, firstname.lastname@example.org Assignment 1 – DNA Modeling Specific Goals Create “teachable” and “enjoyable” lessons on bioinformatics suitable for a biology, computer science, or mathematics class. Test these lessons to evaluate effectiveness on college level students. Long Term Goals Instruct K12 teachers in the areas of bioinformatics education. Educate the next generation of bioinformaticists. Goals Assignment Summaries Quotes “Most of the fundamental ideas of science are essentially simple, and may, as a rule, be expressed in a language comprehensible to everyone.” Albert Einstein (1879-1955) German/U.S. physicist “Science can be introduced to children well or poorly. If poorly, children can be turned away from science; they can develop a lifelong antipathy; they will be in a far worse condition than if they had never been introduced to science at all.” Isaac Asimov (1920-1992) US science fiction novelist and scholar Basic Idea The Special Interest Group of Computer Science Education (SIG-CSE) holds a “Nifty Assignment” series at the annual convention. Presenters demonstrate assignments in computer science that have been tested in an actual classroom environment. These assignments follow SIG-CSE’s concept of nifty assignments for all levels of bioinformatics. Step 0: Setup A.Select colors for DNA stalks and nucleotides (A, T, C, G). B.Cut the nucleotide pipe cleaners in fourths. C.Put in AT/CG pairs. Step 1B Step 1D Step 1E Step 2 Step 2B Step 2C 3 minutes 7 minutes 9 minutes 11 minutes 20 minutes 24 minutes 25 minutes 30 minutes 36 minutes Step 1: Create nucleotides Use these steps to create nucleotide pairs. A.Select two pipe cleaner pieces of the appropriate colors to form a nucleotide pair (AT or CG). B.Put in a V-shape with a small overlap ( 1 / 4 ”). Choose a long end and corresponding short end. C.Coil a long end three or four revolutions around the other short end, covering it completely. There should be some extra left over to attach to a stalk. D.Bend the remaining long and short ends 90° to form a T-shape. E.Repeat step 1C with the remaining long and short ends. Step 2: Connect Nucleotides to Stalks Attach nucleotides to stalks to form a “ladder” A.Attach one side of nucleotide to stalk by wrapping extra length around stalk twice (once on the left, and once on the right). Wrap any remaining length around itself. B.Repeat for other nucleotides, spreading evenly across the stalk. C.Attach opposite stalk in similar way. Leave enough room at ends to connect to other DNA strands. Setup Step 3 Step 1C Step 2A Step 1E
By Amy Cowen on April 22, 2013 1:00 PM
April 25 is National DNA Day, a day that commemorates the 60th anniversary of DNA's double helix discovery in 1953 and the completion of the human genome project in 2003. We all boil down, genetically, to chains of DNA—each of us with an individual DNA sequence. Take time this week to talk with your students and kids about DNA, its history, the scientists who helped crack the code, and ways that students at all levels can get hands-on with DNA-related science.When it comes to advancing understanding of genetics and genomics, the discovery of DNA's structure stands as one of the most important turning points in science history. DNA is the blueprint for all organisms, from tiny bacteria to huge whales and long-extinct T. rex dinosaurs.
DNA, and the information it encodes, not only makes each individual organism unique, but also is responsible for certain similarities and traits in groups of organisms. A rose smells the way it does because of DNA. The color of your eyes has something to do with DNA. Whether or not you are at a higher risk of certain health problems may boil down to certain genetic markers you have or do not have. Although genomes (the sum total of DNA needed to encode an organism) are usually copied and acted on in predictable ways, occasionally these mechanisms go awry. Individual stretches of DNA can change or be altered. Transformations, mutations, and other errors in a person's DNA may result in differences in how people respond to a medicine, for example, or may, over long evolutionary time, result in entirely new species.
Encoding the template for a whole organism sounds like a lot of responsibility for a single kind of molecule, but deoxyribonucleic acid (DNA) does just that!
Finding the Double Helix
There were many scientists involved in identifying and isolating DNA and tying it to understanding of heredity and chromosomes. The history of DNA-related discoveries and breakthroughs dates back to the first isolation of DNA by Friedrich Miescher in 1869. Miescher extracted a DNA sample from cast-off, pus-covered bandages. It sounds kind of gross, but Miescher's discovery fueled further research and inquiry. Until the structure of the DNA molecule was established and modeled, however, scientists were unable to fully explain and further explore the role of DNA.
That all changed in 1953.
The publication of both Photo 51, an x-ray diffraction photo (taken in 1952) showing the crystalline structure of DNA, and of a series of papers describing the structure of DNA in Nature in 1953 was a pivotal moment in science. Photo 51 was taken by Rosalind Franklin, a scientist working to create a crystal of the DNA molecule that would enable x-ray diffraction studies and, she hoped, enable her to deduce the structure of DNA. The x-ray pattern captured by Photo 51 revealed, for the first time, the ladder-like structure and winding helix shape we now associate with DNA.
The findings published in the same 1953 issue of Nature as Franklin's photo were from James Watson and Francis Crick. After seeing Franklin's photo, Watson and Crick were able to make a model of DNA that showed the molecule's structure. In 1962, Watson, Crick, and Maurice Wilkins shared the Nobel Prize in Physiology or Medicine for their research on DNA. (Franklin, whose photo may have cracked the code, died in 1958, her contributions then largely unacknowledged.)
April 25 is National DNA Day, a day that commemorates the 60th anniversary of the double helix discovery in 1953 and the completion of the human genome project by the National Human Genome Research Institute (NHGRI) in 2003.
Breaking It Down
You may have played with a model of the DNA structure, or maybe you wear a visual representation on a t-shirt or have a poster or model hanging on your bedroom wall. A helix is defined as "an object having a three-dimensional shape like that of a wire wound uniformly around a cylinder or cone." In most DNA, two helical strands are wound together creating a double helix. Individual DNA molecules (or strands) are each constructed of two long polymers, chains of repeating units made up of pairs of four nucleotides that appear in various repeating combinations. These nucleotides are adenine ("A"), thymine ("T"), guanine ("G"), and cytosine ("C"). These letters give scientists the ABCs (or ATGCs) of DNA—it's a four-letter alphabet which underwrites all known life on Earth!
Armed with knowledge of the structure, composition, and pattern of DNA strands, scientists are able to tackle questions both about history and about the future. Students can, too!
Students "Do" DNA
From fun home activities that let students and parents explore (and show off!) their own DNA to sophisticated projects for advanced student exploration, Science Buddies has a range of Project Ideas that enable students to better understand the role of DNA and encourage them to explore questions related to genetics, genomics, biotechnology, and bioinformatics. You might be surprised at what your fruits and vegetables drawer will yield in terms of visible DNA discovery, but that's just the tip of the genome!
Some DNA-related Science Buddies Project Ideas to explore:
Extend the Conversation
There are still questions for scientists to ask and answers to be unlocked through further study of DNA. Just last year, samples of DNA with four strands were discovered. See this article in Nature to shake up your understanding of DNA just a bit. What happens when you square or quad your genetic code?