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Three Dimensional Protein Structure and Ligand Binding

Graduate Fellow John Yamauchi & Teacher Partner Dominic Dirksen

Students will synthesize a protein as individual amino acids and function as a catalyst.

Enzymes: 3-D Structure and Function

Understanding how enzymes function is extremely important for developing medical treatments and technologies. This Enzyme 3-D Structure and Function Activity is designed for high school biology students and familiarizes them with features of protein structure that determine its function. The overall activity consists of three portions: 1st is an Introductory Presentation, 2nd is a Kinesthetic activity, and 3rd is a 3-D Structure Visualization. The Introductory Presentation sets the tone for the activity and gives the students background on proteins and amino acids. It also introduces enzymes and their various physiological functions. The Kinesthetic activity presents the students with the challenge of folding a protein correctly. They each will represent an amino acid and will form a polypeptide chain by holding hands with each other and form the lowest energy conformation. The 3-D Structure Visualization allows students to see a molecular view of an enzyme and its active site from an atomic perspective. Students will be assessed with a survey that questions what they knew prior, what they learned, and what they want to know more about. 

Duration: 60-95 minutes

Learning Objectives:

Students will understand

  • What proteins are made of and how they are chemically structured in general
  • An enzyme is a special class of proteins that can perform catalytic reactions converting substrates into products
  • Catalysts are not consumed in the reaction but are reused
  • The active site is necessary to performing this function but can be disrupted by inhibitors or mutations
  • The SHAPE of a protein affects its FUNCTION
  • Changing the enzyme’s environment will alter its function

Students will be able to

  • Open files to visualize protein structures from the Protein Data Bank http://www.PDB.org
  • A how-to guide on PDB

Documents: 

Teacher Guide (doc)

Teacher Guide (pdf)

Student Handouts (pdf)

Sea Urchin Fertilization and Development Activity

In this activity the students will learn about model organisms and cell development by fertilizing sea urchin eggs and monitoring their development. Sea urchin embryos are used as a model organism in Amro Hamdoun’s lab at the Scripps Research Institute at UC San Diego to study a class of proteins called ABC-transporters. These proteins are important for effluxing toxic chemical substrates from cells and also cause certain cancer cells to become resistant to chemotherapy. Sea urchin growth and development can be easily seen with a simple light microscope and the main stages of embryogenesis can be monitored over a few days. The extraction of sperm and eggs from sea urchins is relatively easy and if done appropriately, the urchins can be recycled to collect gametes multiple times. Briefly, the students will fertilize Lytechinus pictus urchin eggs and observe the changes in cellular morphology over time. They will describe and illustrate what they observe throughout the two day activity. Incorporating inquiry into the activity, the students will then make serial dilutions of the sperm and observe any differences in fertilization when these dilutions are added to the eggs. Students will be assessed by answering questions at the end of each section that requires them to make and record their observations. This activity is a modification of multiple sea urchin fertilization protocols.

Duration: Day 1: 60-90 minutes

Day 2: 60-90 minutes

Learning Objectives: 

Students will understand

  • Research with model organisms provide insight into biological discoveries in humans
  • The Processes of fertilization and development in sea urchins is similar to the processes in humans
  • Sperm concentration is important for fertilization to occur
  • Chemical contaminations in the environment can have negative influences on wildlife reproduction

Students will be able to

  • Identify and rationalize the use of suitable model organisms for research
  • Pose a biological/scientific question and propose experiments with model organisms to provide an answer 

Documents

Teacher Guide (doc)

Teacher Guide (pdf)

Student Handouts (pdf)