Carnegie Mellon

NSF Grant DMR 0520425

High School Teachers Summer Internship

Introduction Objective Part I Part II Part III	Introduction Using the 5-E model, this unit emphasizes · determining the molecular structure of molecules; · using models to visualize molecules, and · discussing how computer simulations predict likely protein shape. A central tenet of biology is the relationship between structure and function. This unit examines the molecular shape of proteins. Proteins do most of the work in cells and the function of proteins is determined by their structure. Throughout the unit, students are asked to think about what they know and to question what they are learning as they construct their understanding of molecular structure. This interdisciplinary unit unites physics, chemistry, and technology from a biological perspective. In part one, students are introduced to X-ray diffraction, one of the two techniques for determining DNA and protein structure. In part two, students explore how the data from X-ray diffraction is used to make both computer models and physical models. Finally, in part three students review modern computer techniques for predicting protein shape. Part 1 Using X-ray Diffraction, Material Science Researcher, Rosalind Franklin Determines the Molecular Shape of DNA Introduction Typically, biology books show a picture of Rosalind Franklin’s X-ray diffraction picture of DNA. This picture shows what looks like spots arranged in an X. The photography provokes several questions including: How was this picture made? What does the picture mean?” Part 2 Physical Models/Computer Models Introduction To understand, X-ray data, scientists build models. For example, Watson and Crick’s physical model of DNA is currently found in almost every biology textbook. Today, computer programs such as Rasmol generate complex protein models. From the information provided by computer models, scientists construct physical models. To enhance student understanding of the complex computer models, students first work with physical models before they move to manipulating the more abstract computer models. Part 3 Computer Predictions Introduction Due to various difficulties with crystallizing proteins for X-ray diffraction, scientists today also use computer programs to predict which proteins are most likely to produce a thermodynamically stable protein structure. Monte Carlo and Rosetta are two of these computer programs.
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	Objective Part I · Define X-ray diffraction · Summarize how X-ray diffraction is used to determine structure · Trace the history of X-ray diffraction including the people involved in its development and the evolution of the technology · Explain why molecules in X-ray diffraction need to be crystals · Summarize how X-ray diffraction was used by Rosalind Franklin to determine DNA structure.
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	Background Part I In 1895, W.C. Roentgen discovered X rays. In 1912, Max von Laue discovered X ray diffraction by crystals. Just one year later in 1913, William Bragg reported the crystal *structure of NaCl. Bragg’s Law, nl = 2d sinq , is the mathematical formula for determining crystal shape.
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	What You Need Part I · Flashlights · Shapes 2-D & 3-D · Nylon mesh · Crystals · LED lights · ICE Kit # 90-002 Optical Transfer Kit · ICE Kit # 99001 DNA Optical Transformation Kit · Background Sheets-- “X-rays”, “crystals”, “diffraction”, “wavelength”, “W. Roentgen”, “W. Bragg”, “Bragg’s law” and “world and scientific dates”. · Nova video- “Photo 51” · Crystal models · Pictures of X-ray diffraction machines · Internet connection—website- · Reprint from Nature for R. Franklin’s article and Watson and Crick’s article.
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format

Procedure Part I Engage—Check for prior knowledge Using the human arm as an example, the teacher quickly reviews the anatomical difference between structure and function. The students can then generate their own examples of structure and function. Next, the teacher gives students examples of atoms and molecules on post it notes. The students are asked to identify their atom or molecule as an atom or molecule by placing their atom or molecule on a chart labeled atom or molecule. Finally, the teacher refers to a wall chart that compares the size of different items and asks the students to give the structure for a particular object and to explain how they know the structure. The teacher ends this review by asking students if anyone has seen DNA. The teacher questions the students regarding the shape or structure of the DNA molecule and how the structure is known. Time: 1 class Rationale—In this unit, students need a working knowledge of the terms, structure, function, atom, and molecule. The unit begins by identifying students’ use of these terms and then gives students a chance to review the terms. The engage section of the unit concludes by introducing the question of how we know the shape of things that are too small to see even with an electron microscope. Explore – Wall shadows Students use inquiry to study the shadows on a wall. In groups, students shine flashlights on a variety of shapes. After they draw their experimental set up and record their observations, students share their observations with the class. Students then change one item in their experimental set up. Students record the change in their notebooks and share with the class why they made that particular change and what they noticed. Students are then asked if they can use the shadow to determine size using paper, rulers and meter sticks. Again, students draw their experimental set up, record measurements and share their observations with class. The engage section concludes with a class discussion. Students generate ideas about how this method of determining size can be used to determine the structure of things that are too small to be seen. Time: 2 classes Rationale: In this explore section, students begin to think about the questions and problems, including quantitative observations, that the people initially designing X-ray diffraction encountered. Later in the unit, this investigation will provide the experiential basis for students to compare and contrast their experience of determining size to the actual process of X-ray diffraction. Safety: Caution students to point flashlights on walls not toward each other. Explore—Optical Transfer Kit Working as a unified class, the teacher shines a laser pointer through a lattice pattern on a 35 mm slide from ICE kit # 90-002 Optical Transfer Kit. Continuing from the previous day’s assignment, students ask about making various changes to see what happens to the pattern. After investigating these changes, students will draw the patterns. Looking at one pattern at a time, students will be asked to match the projected pattern with the series of lattices that they have at their desks. Students explain their selected match by making a claim with evidence and reasoning. Time: 1 Class period Rationale: The optical transfer kit builds on the inquiry with the flashlights and gives students additional information as they try to make sense of what they are seeing. Students will observe that the lattice patterns suggest a regular crystal pattern. Safety: This activity is done as an entire class to prevent any lasers from being pointed at another student’s eye. Explain—How is X-ray diffraction used to determine molecular structure? The teacher reviews the meaning of the word “symposium.” In groups of three, students research different topics to determine how their assigned topic relates to the story of X-ray diffraction. The topics include the following: “X-rays”, “crystals”, “diffraction”, “wavelength”, “W. Roentgen”, “W. Bragg”, “Bragg’s law” and “world and scientific dates”. Based on their work with the assigned term, students design a product of their choice that demonstrates what they have learned about their specific topic. Students will present and explain the product they have developed at the symposium. Time: 3-5 classes At the symposium, students present their topics as their classmates collect information from each group. Both students and the teacher will ask the presenters questions about their projects to make sense of the individual topic and how it fits in the larger story. Time: 1-2 classes At the end of the unit, students write a short essay where they explain how X-ray diffraction works. Students will check their understanding either by reading a class essay or by watching a power point about how x-ray diffraction works. Time: 2 classes Rationale: The jig sawing and the symposium teaching techniques are used to ensure that students have developed their understanding of X-ray diffraction at a deeper level of learning including application. X-ray diffraction is a complex topic. Through the jig sawing, students enhance and solidify their learning by creating a product and a platform for sharing their learning with their classmates. Elaborate – Photo 51—Historical X-ray diffraction Students use slides from the DNA optical transfer kit, ICE Kit # 99001, to study DNA shape. Students then view selections from the NOVA video about Rosalind Franklin and her use of X-ray diffraction to determine the structure of DNA. Afterwards, students use the web tools on the NOVA website to analyze photo 51. Time: 2 classes Rationale: Photo 51 is Rosalind Franklin’s famous X-ray diffraction picture of DNA, which is shown in most textbooks as evidence for the double helical nature of DNA, As a result of their direct, hands-on experience, students will have a way to make greater sense of Franklin’s historic image of DNA. Elaborate-CMU-Modern X-ray diffraction Through distance learning, students interact with a scientist or researcher who uses X-ray diffraction. This interaction with a scientist currently using X-ray diffraction reinforces and tests students’ understanding of X-ray diffraction. Time: 1 classes Rationale—X-ray diffraction is still relevant to both biologists and material science scientists. This segment shows X-ray diffraction is being used in a contemporary setting. Additionally, the lesson demonstrates that a tool, such as X-ray diffraction, may be used in different places at different times for a variety of purposes. In fact, Rosalind Franklin studied coal using X-ray diffraction before she began studying DNA. Finally, by exposing students to local scientists working in the field, this section gives students an opportunity to consider the training, skills and experience needed for a future career in the sciences. Evaluate Students select one of the following topics and write an essay. · Explain the collaborative nature of science using the development of X-ray diffraction as an example. · Trace Rosalind Franklin’s study of DNA using X-ray diffraction. Rationale—An understanding of either of the two essay topics demonstrates the students’ comprehension of how X-ray diffraction works and the collaborative nature of science.

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	Lesson Plans Part I National Educational Technology Standards Content Standard A1: Ability to do scientific inquiry Content Standard A2: Understanding of scientific inquiry Content Standard B2: Structure and properties of matter Content Standard C2: Molecular basis of heredity Content Standard E2: Understanding of science and technology Content Standard G1: Science as a human endeavor Content Standard G2: Nature of scientific knowledge Content Standard G3: Historical perspectives
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	Objective Part II · Investigate the chemical interactions between amino acids · Apply chemical interaction rules to model building · Study physical models of proteins · Manipulate computer models of proteins · Explain the relationship between structure and function using a protein of the month from the PDB website Evaluate the relationship between structure and function using the criteria from “SMART” teams
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	Background Part II In 1838, Jons Jakob Berzelius first named and described proteins. In 1839 Gerardus Mulder published the chemical structure of proteins. In 1926, James B. Sumner demonstrated that urease is a protein. Frederick Sanger sequenced insulin in 1854. In 1958, using X-ray diffraction, Sir John Cowdery Kendrew determined the 3-D structure of myglobin, and Max Perutz determined the 3-D structure of hemoglobin. Today the Protein Data Bank, PDB, has over 40,000 searchable protein structures.
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	Lesson Plan Part II Educational Standards used and/or met Content Standard B2: Structure and properties of matter Content Standard C1: The Cell Content Standard E2: Understanding about science and technology Content Standard G1: Science as a human endeavor Content Standard G2: Nature of scientific knowledge Content Standard G3: Historical perspectives
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format		Objective Part III Define probability, thermodynamics Solve problems using a random number generator Review thermodynamics Compare and contrast computer programs, Monte Carlo and Rosetta Review current application of computer programs in predicting protein shape
	Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	Background Part III Monte Carlo refers to computer programs which use randomness to solve complicated problems. In 1945, when computers were developed that could more easily generate random numbers, researchers begin to apply Monte Carlo to many scientific problems and questions. Rosetta refers to a computer program that takes known features of proteins and uses software to predict the shapes of proteins.
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	What Will You Need? Part III · Computers · Computer projector · Internet connection · Websites—Monte Carlo, Rosetta, Stat math random number generator
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	Procedure Part III Engage—Conduct a probability experiment Students will make predictions about the chances of flipping a head in 10 tries. Working in pairs, students will flip their die 10 times and record their results. Students will share their results with the class. Time: 1 class Rationale: The coin flipping activity gives students an opportunity to begin thinking about chance. Monte Carlo works on chance or randomness. Explore— Randomness As a class, students use a Stat Math website to see an example of a random number generator. Students then use another Stat Math website to work a problem using random numbers. Time: 1-2 classes Rationale: Working as a class rather than in small groups, the students benefit from each other’s insights and the teacher’s questions. Explain—Thermodynamics Briefly review with students the principles of thermodynamics and how thermodynamics relates to protein folding. Mention that proteins quickly fold. Time: 1 class Rationale: Thermodynamics is a vast topic. This section focuses on explaining the role of thermodynamics in explaining protein shape. Elaborate—Predicting Protein Shapes Use Yue Chu Brownian motion program as an example of Monte Carlo. Complete a compare and contrast table about the Monte Carlo and Rosetta programs. Rationale: This section gives students an overview of the mathematics and science involved in using computer programs to determine protein shape. Time: 2 classes Evaluate—Success stories Through distance learning, students talk with researchers who are actually using the computer programs to predict protein shapes. Time: 1 class Rationale: Talking with the researcher provides students with the practical context for understanding the use of computer modeling to predict protein shapes.
		Carnegie Mellon NSF Grant DMR 0520425 High School Teachers Summer Internship

Introduction Objective Background What you will need Procedure Lesson Plans Entire lab in .pdf format	Lesson Plans Part III Educational Standards used and/or met Content Standard A12 Understanding about scientific inquiry Content Standard B5: Conservation of energy and increase in disorder Content Standard C1: The Cell Content Standard E2: Understandings about science and technology Content Standard G3: Historical perspectives