TEL Lesson Plan
Investigation of Selected Proteins from a Bioinformatics Database.

Grade Level: 11-12
Subject: Upper Level or Advanced Placement Biology or Chemistry
Time Frame: 2 90-minute class periods, plus independent work


According to, Bioinformatics is defined as "the use of computer science, mathematics, and information theory to model and analyze biological systems, especially systems involving genetic material". Students will use a bioinformatics database called the Protein Data Bank (PDB) to examine the features on six proteins isolated from marine species. This part of the lesson focuses on the research paper for these proteins.

Databases/Other Resources

General Science Collection; Student Edition; Protein Data Bank (


Part I: IDENTIFY THE PROTEIN: 1. Direct your browser to the Protein Data Bank website ( 2. Expand "Educational Resources" in the left panel on the home page. 3. Click on "Exhibit Materials" located on the top menu bar. 4. Click on the Flash Animation under the PDB exhibit for the Birch Aquarium. PART II. RESEARCH 1. Perform a short literature review on that protein selected from the PDB using the General Science Collection from the TEL database. Use appropriate citations in MLA format. 2. Include the following information about the selected protein: The name of the protein; The name of the species from which the protein was obtained; What method was used to analyze the protein? What are the implications of this protein on human life?


Steps for Teacher

NOTE: These procedures are only a part of an overall project.  From the PDB, the student may construct a 3-D model of a portion of the selected protein, including the amino acid sequence.  However, this part uses data and information from the PDB.  A teacher may wish to continue this part of the project by delving into the features and tutorials of using the PDB or, as suggested by this lesson, only use the PDB to get the names of the proteins as described in the procedures and write the research report using sources from TEL.

Glycoprotein from Eelpouts

Thermophilic Proteins from Thermophiles around deep sea vents

Green Flourescent Protein (GFP) from Aequorea victoria a type of jellyfish

Aplyronine A-Actin protein from the Japanese sea hare

Myoglobin from sperm whales

Antigen receptors from a variety of shark species

Steps for Librarian

Steps for Student

Related Activities

Content Standards

Biology II: Standard 4.0 - Heredity

Conceptual Strand 4: Organisms reproduce and transmit hereditary information.

Biology II : Embedded Mathematics

Conceptual Strand: Science applies mathematics to investigate questions, solve problems, and communicate findings.


Learning Expectations/Grade Level Expectations

Biology II: Standard 4.0 - Heredity

Course Level Expectations:

CLE 3216.4.4 Describe the relationship among genes, the DNA code, production of protein molecules, and the characteristics of an organism.

CLE 3216.4.5 Explain how the different shapes and properties of proteins are determined by the type, number, and sequence of amino acids.

CLE 3216.4.6 Explain how the genetic makeup of cells can be engineered.


Biology II : Embedded Mathematics

Course Level Expectations:

CLE 3216 Math.1  Choose, construct, and analyze appropriate graphical requresentations for a data set.

Performance Indicators State

N/A for Biology II


Below is a link to a rubric that can be used for assessment.

ISTE Computer Literacy and Usage Standards

3. Research and Information Fluency. Students apply digital tools to gather, evaluate, and use information.

4. Critical Thinking, Problem Solving, and Decision Making. Students use critical thinking skills to plan and conduct research, manage projects, solve problems, and make informed decisions using appropriate digital tools and resources.



AASL Standards for the 21st Century Learner

1. Inquire, think critically, and gain knowledge.

1.1.5 Evaluate information found in selected sources on the basis of accuracy, validity, appropriateness for needs, importance, and social and cultural context.

1.1.6 Read, view, and listen for information presented in any format (e.g., textual, visual, media, digital) in order to make inferences and
gather meaning.

1.4.1 Monitor own information-seeking processes for effectiveness and progress, and adapt as necessary.

2. Draw conclusions, make informed decisions, apply knowledge to new situations, and create new knowledge.

2.1.2 Organize knowledge so that it is useful.

2.1.3 Use strategies to draw conclusions from information and apply knowledge to curricular areas, real- world situations, and further investigations.

2.1.4 Use technology and other information tools to analyze and organize information.

3. Share knowledge and participateethically andproductively asmembers of ourdemocratic society.

3.1.5 Connect learning to community issues.

4. Pursue personal and aesthetic growth.

4.1.4 Seek information for personal learning in a variety of formats and genres.