Lesson 1 – Scientists Prepare and Plan

Description: Students should complete these lessons near the end of a genetics unit. Typically students would have learned that organisms (and individual cells of multicellular organisms) respond to their environment by changing which proteins they make.




Course:  Biology, Genetics, Biotechnology, Environmental Science

Unit:  Genetics and Heredity

See the NGSS listed in buttons on the upper-left of this page. Also, see the Standards Addressed page for more information and all NGSS and WA State Standards (Science, Math and Literacy) addressed in this module.  In addition to the aligned standards, for this lesson, here is a breakdown of:

What Students Learn:
  • Observations lead to hypotheses and experimental design.
  • Halobacterium (Halo) respond to changes in their environment, such as the amount of light.
What Students Do:
  • Students use scientific thinking to consider how the environment impacts gene expression and cellular networks.
  • Students conduct research into current Halobacterium observations and make a list of possible variables (which leads to lesson 2).



Pacing Guide

Instructional Activities: (One 50-min period, with a bit of homework if needed)

Before beginning lesson: see Advanced Prep for help with lab set up and advance preparation for this and other lessons.

Teacher Background Information:

Students should complete these lessons near the end of a genetics unit.  Typically students would have learned that organisms (and individual cells of multicellular organisms) respond to their environment by changing which proteins they make.  A major way they do this is by regulating ”gene expression” through control of transcription.  Some genes are “turned on” to make mRNA for their corresponding protein, and some genes are “turned off” to stop making mRNA for their corresponding protein.  This allows the cell to conserve energy by producing only what is needed at that time.

This is usually studied in high school classrooms in a fairly artificial situation.  E. coli bacteria are transformed by adding plasmid DNA, and their environment is changed with the addition of the molecule arabinose.  The gene for green fluorescent protein (GFP) is “turned on” (transcribed) in the presence of arabinose and “turned off” (not transcribed) in the absence of arabinose.  This serves as a good model system to study these processes, but E. coli bacteria in nature do not have the gene for GFP, and they do not respond to the molecule arabinose in this manner.

To study this in a more natural situation where an organism’s DNA is not altered, we will use the model system of Halobacterium (Halo), which lives in high salt environments such as the Great Salt Lake.  This module will give students a way to act as scientists as they study how this organism responds to changes that occur in its natural environment.  They will use networks as part of their experimental process in the same way scientists use networks to hypothesize, model, and predict cellular responses to environmental cues.

1. Warm-up:  Pass out a pre-assessment worksheet (Pre-assessment document) (Google Doc | Word Doc) Encourage students to put an answer down for each question even though they may not know the answer. (Pre-assessent Key) (Google Doc | Word Doc)

Lead a class discussion based on questions they may have and specifically lead them into this question: In what ways do cells respond to their environment? Discuss also, why this is especially important for people to study today.  (Today’s youth will have more information about their cells and genomes than previous generations, therefore the interplay between cells and the environment is even more important to understand and consider.)

  • NOTE:  Question 1 of the pre-assessment is designed to see if students are familiar with the concept of networks.  If students need to learn about or review networks, there will be time after the lab is set up (lesson 2).  Complete the Introduction to Systems Module if needed.  Also, see lesson 1 of the Introduction to Systems Module for more information on networks.
  • Question 2 is one of Page Keeley assessment probes for testing whether or not students understand that systems are comprised of interactive parts.
  • Question 3 ascertains if students are familiar with the three types of data analysis involved in lesson 3.
  • Questions 4 and 5 are designed to see if students are familiar with experimental design.  Q4 has too many variables to be useful and in Q5 students should recognize that repeatability confirms data.
  • Questions 6-10 will give you an idea of how much students understand about using model organisms to better understand the interplay between the environment and the genome.
  • Question 10 will give you an idea of how students perceive the turning on and off of genes and what causes this.  The example matches bacterial genetics.  However, Halobacterium is not a bacteria, but an Archae and processes its genome in a similar way to eukaryotes.  For a good review of gene expression in prokaryotes and eukaryote, see this resource:  http://www.nature.com/scitable/topicpage/gene-expression-14121669.

2. Phenomenon Introduction:  PowerPoint (Environmental Influence on Gene Networks Introduction.ppt) (Google Slides | PowerPoint)

Use slides 2 –7 to get students thinking about the importance of gene expression and genetic control. Printable script. (Google Doc | Word Doc)

  • Slide 2:  Define “dynamic” for students as “ever-changing.”  Allow students to offer other “whole body” changes (e.g. hair changing to grey with age, eye color changing from birth, other pre-programmed changes such as hair turning curly after puberty, or changes resulting from diseases such as the formation of cancer) and point out that if the whole body changes, and the whole body is made of cells, then cells must be changing also.
  • Slides 2-7:  Skin cells change by producing more melanin in response to the sun’s radiation.  Sunburn is the body’s reaction when DNA is directly damaged by UV-B light.  The damage triggers DNA repair and the production of melanin (a photo-protectant pigment) for preventing future damage.  Melanin takes UV photons and turns them into harmless amounts of heat.  The damage results in restored DNA, the replacement of new skin cells with a higher level of melanin.
    • Caterpillars and flamingos (shrimp) reflect color of their food source.   Both of the caterpillars are Helicoverpaarmigera.  Which plant the larva feeds on influences coloration.  See ‘bioone.org’ research article
    • Flamingo feathers obtain their wonderful rosy pink color from pigments in the organisms they eat. The flamingos’ feathers, legs, and face are colored by their diet, which is rich in alpha and beta carotenoid pigments. Carotenoids in crustaceans such as those in the flamingo diet are frequently linked to protein molecules, and may be blue or green. After being digested, the carotenoid pigments dissolve in fats and are deposited in the growing feathers, becoming orange or pink. The same effect is seen when shrimp change color during cooking. The amount of pigment laid down in the feathers depends on the quantity of pigment in the flamingo’s diet. An absence of carotenoids in its food will result in new feather growth that is very pale; the existing pigment is lost through molting.  San Diego Zoo Flamingos
    • Drosophila wings: curly is a mutant and will develop as straight wing if pupated at 16 degrees Celsius. Genetics.org reprint (Lenore Ward)  see pages 1-5
    • Hydrangeas respond to pH of soil.
      • Flower color in H. macrophylla is dependent on cultivar and aluminum availability. Aluminum is necessary to produce the blue pigment for which bigleaf hydrangea is noted. Most garden soils have adequate aluminum, but the aluminum will not be available to the plant if the soil pH is high. For most bigleaf hydrangea cultivars, blue flowers will be produced in acidic soil (pH 5.5 and lower), whereas neutral to alkaline soils (pH 6.5 and higher) will usually produce pink flowers. Between pH 5.5 and pH 6.5, the flowers will be purple (see image at left) or a mixture of blue and pink flowers will be found on the same plant.
      • http://www.usna.usda.gov/Gardens/faqs/hydrangeafaq2.html
    • Twins develop different fingerprints in response to the uterine environment.  While identical twins grow in the same uterus and have identical DNA, the placement within the uterus is different which impacts the specific formation of fingerprints.
    • This provides key evidence of the importance of even small environmental changes having large effects on gene expression.  We can see this manifested in the organism’s phenotype.
  • Slide 8 (Flow of Information) reminds students of how DNA results in proteins.  To answer the ‘whys’ on the previous slides, ask students to consider where in the flow of information a change would have to occur in order to get a different protein.  (Teacher note:  transcription most likely answer)
  • Slide 9 asks students to think of ways a scientist might test how the environment influences gene expression.  Lead students through the questions.  Brief answers:

1)    The cell must conserve as much energy (and nutrients) as possible and does this by only making the proteins it needs, when it needs them.  Said another way, backing up from protein synthesis to the gene level, it only expresses the genes it needs, when it needs them, to save energy.  Use analogies that make sense to your students, such as, if you have 4 homework assignments due this week, you will do the one tonight that is due tomorrow instead of doing them all at the same time when that is not needed.

2)    Cells are surrounded by membranes that are typically semi-permeable.  Their local environment is the solution they are in and this changes according to diffusion/osmosis, etc.  These cells are packed in an increasingly larger environment (similar to stackable wooden dolls) that is also permeable to the outside environment.  Ways our environment impacts us: through our openings (mouth, nose, eye sockets, etc.) and even through our skin if it has a cut or even if it’s not damaged, as is the case with u-v waves.  Cells are susceptible to the outside environment.

3)    Cells change in response to stimuli from the environment.  Examples of cellular responses: movement of materials through pumps, diffusion, etc. or the movement of the cell itself via cilia, a flagellum, etc. or a change in gene expression to make a new protein or to stop or change the amount of current protein synthesis.

4)    We can put cells into an environment and systematically change that environment and measure how the cell responds.  A few examples of ways to measure that change include gene expression changes via microarray, position of cells, and growth of cells or populations.

  • Slides 10-12 (Model Organisms). Discuss the use of model organisms such as fruit flies or mice.  Since changing the environment on an observable level can be difficult with a complex, multi-leveled organism, we can use model organisms.  Halobacterium is, in particular, a model organism for both experts and beginning scientists due to its non-hazardous nature.
    • NOTE:  Fortunately for research scientists, biological processes have been found to operate exactly the same in many different organisms. The “Krebs cycle” (the process cells use to extract energy from sugars) is the same across most species. Hemoglobin (essential for blood to carry oxygen to cells) is the same across different species of vertebrates. Because biological processes operate the same in various species, including both very simple and very complex life forms, scientists can use simpler organisms for their initial studies of biological systems.
    • We call this sort of simpler study case a “model organism”. The simplicity of a model organism allows a scientist to more easily zero in on the properties and functions of interest, without having to sort out the complexity arising from additional systems embodied in more complex organisms. For instance, scientists can study yeast cells to understand how sugars are metabolized in many species (including in humans), without having to deal with the additional complexity from other systems in complex organisms (such as contracting muscles). Moreover, small organisms (such as yeast cells) reproduce quickly, allowing biologists to study multiple strains and generations of an organism in a short time.
    • Model organisms are carefully selected to provide simple cases for our initial studies of biological systems. They simplify our initial research, yet still provide data-rich and flexible experimental “systems” for us to examine. They are vital to our initial biological discoveries. Research findings from model organisms must be confirmed by also studying humans. But studies on model organisms are crucial to eventually answering the central biological questions regarding human life.
  • Slide 13 (Exploring how Halo…) Discuss possible variables as per slide.  The picture is of South Bay Salt Pond restoration project (near San Francisco).  You can go to “Google Earth” to get a great view of the entire area.
Teacher Note:  Halobacterium salinarum (Halo) is not a moneran (bacteria) but belongs to Domain Archaea.

Career Connection that extends this science content: Here is a short video prepared by scientist, Karlyn Beer, that may be both fun and helpful for students: http://www.youtube.com/watch?v=w-wEA4DAE3g.  Also, this news piece (ISB Molecular Me: Domesticated Microbes), based on a scientific, peer-reviewed article, is useful for students to read to get an appreciation of model organisms.  This article also helps links these lessons to important evolutionary concepts.

3. Student Experimentation Planning – Give each student the “SCIENTISTS PREPARE AND PLAN: HALOBACTERIUM EXPERIMENTS AND RESEARCH” worksheet. Outline parameters for their research, such as appropriate sites and citations as they look for information on the internet.  The following is helpful information to get students started when searching the internet:

  • The wild type strain that is an ideal model organism goes by several names
    • Halobacterium salinarum (name is italicized or underlined)
    • Wild type Halobacterium
    • NRC-1
  • Good search phrases:  Search the various names above or also “Halobacterium natural conditions”, “Halolophiles environment” or “Halophiles natural conditions”
  • Other key words that can be used (some alone, some together):  Archaea, salt-loving, model organisms, Salt Lake Ecology, Microbiology, halobacteria, high salt environment.  See the list below (in resources) for useful scientific papers and website.  While some papers may be a stretch for students to fully understand, they can be used as a way to begin viewing scientific literature and to scan for needed pieces of information.
  • As students are researching, instead of getting frustrated by not understanding all of the terms, remind them to break words apart and to associate them with known words.  Certain words should make them think of certain environmental conditions, such as
    • Photo = light, UV radiation = light, light driven pump = a pump that works with light
      • So when they see “phototaxis”, or “photosynthesis” in reference to Halo, they might consider the idea of incorporating light and dark as an environmental condition to study.
    • Fermentation = anaerobic process; whereas “oxidative” (or the like) probably involves oxygen
    • Chemo = chemicals or food in this case, so chemotaxis involves moving towards food
  • If students consider the natural environment, they’ll probably come up with pollution as an environmental factor that can change gene expression.  If that is the case, steer them towards metal pollution which is common – you could experiment with nickel and iron easily.
    • Nickel pollution comes from: Diesel fuel and gasoline (exhaust), lubricating oil, metal plating, bushing wear, brake lining wear, asphalt paving
    • Iron pollution comes from: Auto body rust, steel highway structures (guard rails, bridges, etc.), moving engine parts
    • Copper and other like metals are also possible as are nitrogen and phosphorus

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How will I know they know?

Students should have compiled several possible variables gleaned from their research.  Background information should be written in notebooks and students should be ready to share findings (see lesson 2).  If students need help getting organized before class discussion, have them use a ‘team planner’ sheet when they discuss there ideas with their lab group. Team Plan Sheet (Google Doc | Word Doc)

The preassessment (Google Doc | Word Doc) will also inform you of their entry understanding of key concepts.



If you do not have access to the internet or have students who are not capable of successful searching, print information to hand out.  Or print useful PDFs from the Extremophile Lesson 1 of the Ecological Networks module.

This site has less complex, general information about archaeans and Halo.  It is 2 pages. http://www.ucmp.berkeley.edu/archaea/archaea.html

If students need help getting organized before class discussion, have them use a ‘team planner’ sheet when they discuss there ideas with their lab group.


“Wanted For Being A Model Organism!” Students make a ‘wanted’ poster of an organism used as a model system for research (modification of activity from extensions for “Ecological Networks” Module).  Students could make a ‘certificate for the model organism’ in a similar fashion.  Teacher Tips

“I Can Top That!”  Students compare and contrast what it means to be extreme.

A quick exploration of model organisms.  See lesson 3 extension for an example of how mice with gene knockouts are used to study learning and memory.  (These extensions adapted materials from Dolan DNA Learning Center at Cold Spring Harbor Laboratory)

Picture/Image Acknowledgements: