Biological Shapes

A CIBT Lab Exercise in Chemistry for Biology

Abstract

Abstract

Remember the old salad dressing commercial tag-line "…because oil and vinegar don’t mix!" Water has that same love/hate relationship with many other molecules. Through this series of lessons, students will learn about the properties which make other molecules "love" or "hate" water. They will also begin to build a concept of how molecules derive their shapes when placed in water-based environments such as cellular cytoplasm. The packet is divided into several activities that are described below and are meant to be completed in the order indicated.

I. "Its All in the Shape" - Students use gumdrops and toothpicks to build three dimensional models of simple molecules like water, alcohol, etc. In this exercise students learn that even simple molecules have 3-dimensional shapes even though structural formulas appear to only have two.
II. "To Mix or Not to Mix" – In this lesson, students are provided with an opportunity to make selections, observations, conclusions, and form hypotheses regarding solution miscabilities ("mixabilities"). In the process, students discover what makes a molecule either "water-loving" or "water-hating".
III. Through a demonstration, students will observe the behavior of oil droplets in alcohol. For homework, they will carry out a set of calculations and make some conclusions based on their calculations and their observations from the oil/alcohol demonstration.
IV. As preparation for "As the Molecule Turns," students will use references to learn about five different proteins of their choosing. They will also classify several of the 20 amino acid side chains as either "water-loving" or "water-hating" based on the results of "To Mix or Not to Mix". "As the Molecule Turns" – It is often terribly difficult for students to visualize such things as molecular structure and activity. Technology has developed, however, to a point that CAD programs are now available that can help us "see" molecules in their bonding arrangements. In this activity, students will use a computer program to visualize proteins and to discover how the behavior of "water-loving" and "water-hating" molecules plays an important role in regard to protein shape.

Abstract

Appropriate Levels

Life Science, High School, Honors, or Advanced Placement Biology.

Abstract

Time Required

Three 45 minute in-class periods. Minimal teacher preparation time is required.

Abstract

Materials

"It’s All in the Shape":

  • gumdrops (buy them in bulk and be certain that each group gets at least 12 gumdrops of one single color, 4 of a different color, and 3 of yet another different color. Stale gumdrops work best so buy them and open the bag several weeks ahead of time, if possible.)
  • toothpicks (2 boxes per class, ~12 per pair)
  • scissors (1 per pair)
  • colored pencils.

"To Mix or Not to Mix - That is the Question":

  • Stock bottle of 70 % ethyl alcohol (~ 10 ml per pair - dry gas can be used as a cheaper substitute for alcohol
  • Stock bottle of methyl alcohol (~ 10 ml per pair)
  • Test tube racks (1 per pair)
  • labeling pens (1 per pair)
  • disposable latex gloves (1 per pair of students)
  • safety goggles or glasses(1 per student)Polaroid film type 667 can be purchased in packs of ten exposures (#25 W 1135, $28.85).
  • Metric rulers (needed to complete first homework assignment)
  • calculators (1 per pair; needed to complete first homework assignment) Oil/alcohol mixing demonstration
  • glass petri dish bottoms (2) • 70% ethyl alcohol(~ 40 ml)
  • Cooking oil (~20 drops)
  • dishwashing detergent (~ 5 drops)
  • Overhead projector for visualization

"As the Molecule Turns":

  • Computer equipped with molecular visualization software and coordinate files for myoglobin and collagen. See the supplies page for this lab for tips on obtaining suitable software.
  • Color coded phone cord (Several per class. Purchase 10 ft. phone cords. With the phone cord coiled tightly, divide into 10 more or less even sections. For every other section, use a magic marker to color the cord. The lines you have drawn will represent regions of the polypeptide chain that contain hydrophobic amino acid side chains. Uncolored regions will represent stretches of hydrophilic side chains.)
  • Twisties (~100 per class)

General Lab Supplies

  • 1 or 2 liter flask or beaker
  • Labeling tape
  • 2 liter flask (one per 6 groups of students)
  • 4 markers
  • 2000 ml graduated cylinder (at least one per class)
  • razor blades or scalpels
  • transfer pipettes (5-6 per muscle sample)
  • mortar and pestles (1 per muscle sample)
  • 1 Container capillary micropipettes & 6 stainless steel plungers
  • 1 Spatula
  • glass rods
  • safety glasses
  • Test tubes (16 mm)
  • Latex Gloves
  • Clinical centrifuge or funnel with cheesecloth (one for whole class)
Copyright for this material is held by Cornell University, the Cornell Institute for Biology Teachers (CIBT), the Center for Nanoscale Systems Institute for Physics Teachers (CIPT), and or West Hill Biological Resources, Inc., 2014. This work may be copied by the original recipient from this web site to provide copies for users working under the direct supervision of the original recipient. All other redistribution of this content without the express written permission of the copyright holder(s) is prohibited.

Price:       No Charge

Authors:

Jim Blankenship, Cornell University, Ithaca, NY

Nancy Wright, Honeoye Central School, Honeoye, NY.