CORE MOLIT ACTIVITIES at a glance

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CORE MOLIT ACTIVITIES at a glance 1. Amplification of Biochemical Signals: The ELISA Test http://molit.concord.org/database/activities/248.html The shape of molecules affects the way they function.

Students are introduced to the role of molecular shape, weak attractions and charge in biology and biochemistry, and then undertake a simulated Direct ELISA test. 2.

1 CORE MOLIT ACTIVITIES at a glance 1. Amplification of Biochemical Signals: The ELISA Test The shape of molecules affects the way they function. A test for the body's response to intruders can make use of this. Students are introduced to the role of molecular shape, weak attractions and charge in biology and biochemistry, and then undertake a simulated Direct ELISA test. 2. Atomic Layer Deposition: a window into nanoscale processes. Students undertake a simulation of the Atomic Layer Deposition (ALD) technique, a CVD process in which two complementary precursors (e.g., Al (CH3)3 and H2O) are alternatively introduced into the reaction chamber, and build an atomic scale film. Students experiment with temperature and discover its effect upon irregularities in this process. 3. Chromatography

They manipulate hydrophobic and hydrophilic characteristics of the mobile and stationary phases in order to compare results. 4. Density, Buoyancy and Centrifugation http://molit.concord.

2 Chromatography uses differences in weak attractions among molecules to effect molecular separation. Students learn about the phases of molecular separation, mobile and stationary, and then experiment with paper and ion chromatography. They manipulate hydrophobic and hydrophilic characteristics of the mobile and stationary phases in order to compare results. 4. Density, Buoyancy and Centrifugation Because density is a property of a substance, regardless of the amount of that substance, it can be used to separate one material from another. Students explore the relationship between atomic mass, volume, and density, and relate these to the technique of centrifugation. They analyze the impact of temperature on centrifugation.

critical to its shape and function. 6. Diffusion, Osmosis and Dialysis http://molit.concord.org/database/activities/223.

3 5. Designer Proteins (follows # 8) A protein's structure enables it to perform particular functions. Students experiment with code for DNA that translates into proteins, specify how coding of protein relates to desired protein sequence, and demonstrate how the distribution of charge in a protein is critical to its shape and function. 6. Diffusion, Osmosis and Dialysis Materials such as water, nutrients, dissolved gasses, ions and waste are constantly moving across a cell's membrane. In this activity, students interact with models of diffusion and osmosis and observe the net flow of molecules in air, in cells, and across a cell's semi-permeable membrane. Students discover that diffusion results from collisions of particles, learn that particles diffuse from high concentration to low concentration, and connect the process to dialysis. 7. Distillation and the Role of Weak Forces

Distillation affords students a way to experiment with phase change, as they change variables such as the strength of van der Waals attractions and repulsions, temperature, and composition of

DNA Hybridization and Southern Blot http://molit.concord.org/database/activities/244.

4 Distillation affords students a way to experiment with phase change, as they change variables such as the strength of van der Waals attractions and repulsions, temperature, and composition of mixtures to see the impact on distillate, compare the separation of different substances in mixtures and discover why some are easier to separate than others. 8. DNA Hybridization and Southern Blot Laboratory techniques such as Southern Blot and fingerprinting make use of the weak attractions that allow DNA to hybridize, or bind to other nucleotides. Students modify short segments of DNA so that they hybridize with other strands, discover the difference between hybridization and denaturation, and discover how these concepts relate to the Southern Blot procedure. They design a DNA probe. 9. DNA to Protein Synthesis (co-developed with Molecular Logic)

information about sequence of amino acids in proteins.

5 The sequence of nucleotides in the DNA serves as a genetic code, dictating the sequence of amino acids in proteins. Students reason how DNA, a linear polymer made of four different types of monomers (adenine, thymine, guanine, and cytosine), can store the genetic code: information about sequence of amino acids in proteins. In addition they describe the processes of translation and transcription; compare the structure, location, and function of RNA and DNA; and manipulate the DNA code and observe how it changes the sequence of m- RNA and proteins. 10. Electrophoresis and SDS Page

html Fluorescence is a glow produced when electrons, which have absorbed energy from a source like ultraviolet (UV) light and have gone to a higher orbital, sink back to a lower orbital, releasing

6 In this activity students explore electrophoresis and the role electrostatic forces and mobility of particles play in the results. Students review diffusion and then proceed to explore several types of electrophoresis. 11. Fluorescence and Molecular Tagging Fluorescence is a glow produced when electrons, which have absorbed energy from a source like ultraviolet (UV) light and have gone to a higher orbital, sink back to a lower orbital, releasing most of the absorbed energy as light of a longer wavelength. Fluorescence has many applications in lighting, mineralogy, and biochemistry. When fluorescent chemical groups are attached to other molecules, they can easily be detected. In this activity students explore how fluorescence works and see its potential uses. Students observe interactions of light and matter, adjust energy levels of electrons, and explore changes in emissions. They create model fluorescent tags in DNA. 12. Introduction to Crystals

Crystals are common forms of solids characterized by the order of the molecules. In this activity students explore crystal structure with their implications for integrated circuit manufacturing.

types of imperfections and predict the effect of defects and grain boundaries on crystal cleavage. 13. Light and Matter Interactions: An Introduction to Photons http://molo.concord.

7 Crystals are common forms of solids characterized by the order of the molecules. In this activity students explore crystal structure with their implications for integrated circuit manufacturing. They investigate the van der Waals attractions, ionic charges and electron clouds that hold various types of crystals together; they melt and attempt to reform a molecular crystal; and they explore types of imperfections and predict the effect of defects and grain boundaries on crystal cleavage. 13. Light and Matter Interactions: An Introduction to Photons Students are introduced to the basic concepts of light, followed by several interactive simulations that model the interactions of light with matter. They manipulate the intensity and frequency of light, adjusting the intensity and seeing its effect on the heating of matter; they replicate in a model a beam of photons of particular intensity and energy; they describe two fates of light-matter interaction -- passage through, or absorption and consequence by matter; and they generate and read an absorption spectrum. 14. Liquid Crystals and LCD Displays

This activity addresses the unique nature of liquid crystal molecules, effectively another state of matter, and how those molecules behave in electric fields.

Students explain how a liquid crystal relates to other states of matter; draw or describe the behavior of liquid crystals in an electric field; and give an overview of how an LCD panel works. 15.

8 This activity addresses the unique nature of liquid crystal molecules, effectively another state of matter, and how those molecules behave in electric fields. They experiment with the effect of polarity of crystals, and the intensity and direction of electric fields on liquid crystals. Students explain how a liquid crystal relates to other states of matter; draw or describe the behavior of liquid crystals in an electric field; and give an overview of how an LCD panel works. 15. Mass Spectroscopy The activity offers students an opportunity to manipulate the central variables in mass spectroscopy, which operates on the principle that moving ions may be deflected by a magnetic field and hence identified. This model demonstrates how the force exerted on each ion depends upon the strength of the magnetic field, the velocity with which the ion is moving, and its charge. Students separate the moving ions according to their mass-to-charge ratios; explore the role of the magnetic field in the deflection of moving ions; and explain why the angle of deflection is proportional to the mass-to-charge ratio. 16. Molecular Crystals Students are introduced to a particular type of crystal, a molecular crystal held together with weak forces. Students compare properties of polymorph crystals as they relate to changes in temperature and pressure; examine and interpret X-ray

$diffraction results of the crystals; and determine the implication of crystal variations in technology. 17. Nanomachines (demo) http://molit.concord.org/database/activities/276.$ Molecular machines differ significantly from macroscopic machines in that they are always in a chaotic environment governed by the laws of thermodynamics.

Molecular machines differ significantly from macroscopic machines in that they are always in a chaotic environment governed by the laws of thermodynamics.

9 diffraction results of the crystals; and determine the implication of crystal variations in technology. 17. Nanomachines (demo) Many biological systems can be thought of as tiny -- but very accurate -- molecular machines that use chemical energy to do certain jobs. Molecular machines differ significantly from macroscopic machines in that they are always in a chaotic environment governed by the laws of thermodynamics. This reality makes it very difficult for us to devise molecular machines that work predictably and reliably. Students interact with nanomachines, compare nanomachines to macroscopic machines, and determine what the nanomachines have in common. 18. Piezoelectric Effect and the Atomic Force Microscope (demo) The piezoelectric effect is the conversion between electricity and mechanical motion. Mechanical forces on piezoelectric materials can produce electricity (e.g., piezoelectric sparkers). Conversely, applying voltage on some piezoelectric materials results in distortion or deformation. For example, piezoelectric ceramic materials have been used to move the tip of a scanning tunneling microscope

(STM). Students can pull the slider to change the voltage and observe the change of the crystal. 19. Polymerization http://molit.concord.org/database/activities/282.

10 (STM). Students can pull the slider to change the voltage and observe the change of the crystal. 19. Polymerization Students explore both polymers and copolymers. They use 2D and 3D models and chemical animations to do this. They investigate both addition polymerization and condensation polymerization, and then compare linear, branched, and cross-linked polymers. They connect the density of polymers with differences in their structure. Finally they connect polymer structures with their ease of destruction, and consider the importance for recycling. 20. Reaction Rates, Catalysis and Pasteurization This activity introduces key ideas of chemistry, including reaction rates, bond strength, activation energy, catalysis, and equilibrium. Students manipulate models to discover how these variables are related. They manipulate reaction rates by changing temperature and concentration, and demonstrate their

understanding by creating an endothermic reaction that releases a lot of heat energy, one that requires a catalyst, and one that reaches equilibrium between reactants and products. 21.

html Students learn the necessary conditions for self-assembly (random motion and molecular stickiness), play with some example models of self-assembling biological structures (quartenary structures

11 understanding by creating an endothermic reaction that releases a lot of heat energy, one that requires a catalyst, and one that reaches equilibrium between reactants and products. 21. Self-Assembly, with Nanomanufacturing Students learn the necessary conditions for self-assembly (random motion and molecular stickiness), play with some example models of self-assembling biological structures (quartenary structures such as hemoglobin, fibers, and microtubules), and then design their own self-assembly structures. They manipulate two key characteristics of molecules that allow them to self-assemble, investigate the effect of temperature on self-assembly, and explore the effect of molecular shape on the larger structures built by self-assembly. 22. Template Based Synthesis and PCR Using DNA's capacity to make many copies of itself, the laboratory procedure Polymerase Chain Reaction (PCR) replicates DNA samples for forensics and drug development. Students learn that it is difficult, if not practically impossible, to create a polymer without some guiding template molecule. DNA is then discussed as an example of template-based synthesis and the basics of DNA replication are explored. Finally, students discover how the natural mechanism

html In this activity, students see that, when a small particle is surrounded by water molecules (or by other atoms/molecules), its resulting motion looks random.

12 of DNA replication can be used to amplify small amounts of DNA using the Polymerase Chain Reaction (PCR) procedure. 23. Thermal (Brownian) Motion: Atoms and molecules are always in motion (linked to Refrigeration) In this activity, students see that, when a small particle is surrounded by water molecules (or by other atoms/molecules), its resulting motion looks random. However, this apparently random movement is due to collisions with many other atoms or molecules, all moving in straight lines until they collide. Students replicate Brown's experiment, in which he discovered Brownian Motion; they discover how temperature influences the motion of particles, and the "random" nature of collisions. They connect these concepts to the process of refrigeration. 24. X-Ray Crystallography (defraction - EMR) This activity introduces the fundamental principles of X-ray crystallography, guiding users through a series of activities for learning the way structural information can be derived from X-ray diffraction patterns. Students discover

what can be detected with X-ray crystallography, proteins in particular, and they explore the impact of temperature, atom size, and impurities on the tests. 25.

html The FACS procedure combines basic science ideas: that some molecules fluoresce, that other molecules selectively bind to molecules within cells, and that electric fields can deflect charged

13 what can be detected with X-ray crystallography, proteins in particular, and they explore the impact of temperature, atom size, and impurities on the tests. 25. FACS (Fluorescence Activated Cell Sorting) The FACS procedure combines basic science ideas: that some molecules fluoresce, that other molecules selectively bind to molecules within cells, and that electric fields can deflect charged particles. Students are helped to understand the basic components of the FACS cell sorting procedure and the science underneath it (fluorescence and separation by charge). 26. Drug Design: Protein Kinases In this activity students investigate what is known about one particular kind of molecule that is a target for new drugs a protein kinase. Students review

protein structure and hydrophilic/phobic interactions, and then study kinases, small proteins that regulate numerous cell processes. 27. Protein Conservation: A View Into Proteomics http://molo.

14 protein structure and hydrophilic/phobic interactions, and then study kinases, small proteins that regulate numerous cell processes. 27. Protein Conservation: A View Into Proteomics Students review aspects of protein structure and folding and then move to 3D molecules, evaluating the consequences of both conservative and nonconservative substitutions in protein sequences. The activity culminates in a comparison of human, rat and bacterial enzymes; students discuss why it is important for some regions to be conserved.

BIOCHEMISTRY GUIDED NOTES - AP BIOLOGY-

BIOCHEMISTRY GUIDED NOTES - AP BIOLOGY- ELEMENTS AND COMPOUNDS - anything that has mass and takes up space. - cannot be broken down to other substances. - substance containing two or more different elements