Molecular Explorations

Ocean Exploration / Grades 9-12 / Life Science, Chemistry

Focus Question

What are some molecular biology techniques that scientists use to explore Earth’s deep ocean?

Learning Objectives

Links to Overview Essays and Resources Useful for Student Research


Audio/Visual Materials


Teaching Time

Three or four 45-minute class periods, depending upon the number of activities selected.

Seating Arrangement

Laboratory groups of two to three students.

Maximum Number of Students


Key Words

Restriction enzyme
Molecular biology


Background Information

In the past twenty years, scientists have explored areas of the deep ocean that have never been visited before. These expeditions have discovered hundreds of new species, and even new ecosystems, but 95% of Earth’s ocean remains unexplored.

Why is it important to explore the deep ocean? Consider this: Most drugs in use today were initially found in living organisms, and almost all of these organisms are terrestrial. Recent systematic searches for new drugs have shown that antibiotic, anti-cancer, and anti-inflammatory substances are much more common among marine invertebrates than among terrestrial organisms. Particularly promising invertebrate groups include sponges, tunicates, ascidians, bryozoans, octocorals, and some molluscs, annelids, and echinoderms (see the Ocean Exploration lesson “Benthic Drugstore” at for more information).

The National Oceanic and Atmospheric Administration (NOAA) created the Office of Ocean Exploration in 2001 to spearhead efforts to learn more about unexplored areas in the Earth’s ocean. Recent expeditions have explored the Submarine Ring of Fire in the Mariana Arc, the New England seamount chain, the Gulf of Alaska seamounts, the Arctic Ocean, the Black Sea, the Galapagos rift, and the Northwestern Hawaiian Islands. Recent accomplishments include bioprospecting for new deep sea medicines, observation and monitoring of a new underwater volcano in Hawaii, testing non-invasive research tools to observe and collect deep-sea samples, and investigation of new species in previously unexplored deep-sea ecosystems.

Many of these accomplishments would have been impossible a few years ago, but innovations in equipment and techniques have given researchers powerful new tools for exploring Earth’s ocean environments. Molecular biology techniques, in particular, are being used to answer questions about ecology, biodiversity, evolutionary genetics and systematics of marine organisms, as well as in prospecting for new natural products that can be used to treat disease. These techniques include DNA extraction, RNA extraction, the use of gel electrophoresis to visualize DNA and RNA, polymerase chain reaction (PCR), and DNA sequencing. This lesson is intended to introduce students to several of these techniques.


Learning Procedure

[NOTE: This lesson is based on activities designed by Ellen Averill, Karen Kyker, Sandy Collins, and Theresa Knapp while participating in the 1993 Woodrow Wilson Biology Institute. These activities are used with permission from the Woodrow Wilson National Fellowship Foundation. Visit for information on other activities and programs. The restriction enzyme activity is obtained from the Access Excellence Classic Collection:]

  1. Download the following activities:

There are two options for obtaining the equipment needed for the electrophoresis activity. The first is to buy electrophoresis chambers and power supplies from a laboratory supply company (cost approximately $400 and up). The second is to build your own chambers and power supplies as directed in the “Desktop Electrophoresis Lab” activity (cost approximately $20 per system).

  1. Prepare detergent/salt solution, meat tenderizer solution, sodium chloride solution, electrophoresis gels, TRIS/Borate/EDTA buffer, and student instruction sheets (from the downloaded activities) prior to the lab. If you want to use the (lower cost) “Desktop Electrophoresis” apparatus, prepare the chambers and power supplies as well, unless you plan to have students do this.

  2. Briefly discuss the fact that much of the Earth’s ocean is totally unexplored, particularly the deepest areas. Highlight some of the discoveries that have been made by recent expeditions to study the deep ocean. You may want to mention hydrothermal vent communities, cold seeps, methane ices, and deep sea medicines. The following Web sites have useful information for this discussion: for a virtual tour of a cold seep community; for a virtual tour of a hydrothermal vent community; and for background on methane ices; and for background on deep sea medicines.

  1. Tell students that recent advances in molecular biology techniques provide powerful tools for many kinds of scientific investigations, from marine research to crime scene investigations. Discuss the ways in which ocean exploration expeditions might use these techniques. Suggestions should include:

Tell students that the purpose of these activities is to introduce three of these techniques.

  1. Have students complete the “Isolation of DNA from Onion” lab activity as directed in the student instructions.

    If you want students to use their DNA isolates for the electrophoresis activity, have them transfer the DNA to a clean test tube, rinse with 70% ethanol to remove excess salts, then pour off the ethanol from the test tube. Add 0.5 ml distilled water to the test tube, cover, and refrigerate until the next day. Each student or student group should record their procedures and results in a lab notebook or written report.

  2. Introduce the technique of electrophoresis using the “Electrophoresis Analogy.” Have students complete the “Rainbow Electrophoresis” lab activity as directed in the student instructions. Each group should prepare written answers to the questions included in the activity, either in a lab notebook or separate written report.

    If you are having students use the DNA extracts prepared in Step 5 for this activity, have them put 85 ml of their extract into a clean test tube, add 15 ml TRIS/Borate/EDTA buffer, and load the electrophoresis gels as directed in the student instruction sheets. Run the gels at 81 volts (use nine batteries in the power supply) for about one hour. Stain the gels by soaking overnight in a 0.02% solution of methylene blue in distilled water. Procedures and results should be recorded in a lab notebook or written report.

  3. Introduce the technique of restriction enzyme cleavage using the word analogy activity described in “How Restriction Enzyme, Probes and RFLP’s Work.” If you want to do an actual restriction enzyme cleavage procedure, visit the University of Arizona’s Biotech Project Web site ( for a list of biotechnology laboratory experiments. The teacher guide and student guide for the Restriction Enzyme Analysis lab can be downloaded from and


The Bridge Connection

The Bridge is a growing collection online marine education resources. It provides educators with a convenient source of useful information on global, national, and regional marine science topics. Educators and scientists review sites selected for the Bridge to insure that they are accurate and current. – Click on “Ocean Science Topics” in the navigation menu on the left, then “Human Activities,” then “Technology”

The “Me” Connection

Have students write a brief essay describing three personal benefits that might result from molecular-level explorations of the deep ocean.


  1. Visit for details of Ocean Exploration expeditions (many with detailed daily logs) and over 150 hands-on, standards-based lesson plans and a curriculum based on the explorations.

  2. For a virtual restriction mapping activity, visit

  3. Biological supply companies have a variety of materials and kits suitable for other DNA research techniques.


Resources – Introductory page for the Ocean Exploration website – Web site for the University of Arizona’s Biotech Project – An animated primer on the basics of DNA, genes, and heredity from the DNA Learning Center at the Cold Spring Harbor Laboratory – Background and activities from the 1993 Woodrow Wilson Biology Institute on Biotechnology

National Science Education Standards

Content Standard A: Science as Inquiry

Content Standard B: Physical Science

Content Standard C: Life Science

Content Standard E: Science and Technology

Content Standard F: Science in Personal and Social Perspectives


Ocean Literacy Essential Principles and Fundamental Concepts

Essential Principle 1. The Earth has one big ocean with many features.

Essential Principle 2. The ocean and life in the ocean shape the features of the Earth.

Essential Principle 3. The ocean is a major influence on weather and climate.

Essential Principle 4. The ocean makes Earth habitable.

Essential Principle 5. The ocean supports a great diversity of life and ecosystems.

Essential Principle 6. The ocean and humans are inextricably interconnected.

Essential Principle 7. The ocean is largely unexplored.


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