How to Turn on Genes
an exploration of differential gene expression
Geneticist: Brinda Rana
Teacher: Sara Dozier
Content Standards:
• California Biology Content Standard 4d: d. Students know specialization of cells in
multicellular organisms is usually due to different patterns of gene expression rather than
to differences of the genes themselves.
Major Concepts:
• Phenotypes are regulated by gene expression.
• Gene expression can be altered by many factors, including (but not limited to)
environment, epigenetics, intercellular signaling, hormones, and signal transduction.
• Review of central dogma, explain misconceptions. DNA => Gene product => phenotype
=> DNA
• Laboratory Notebook Documentation: Maintain an accurate and complete laboratory log
notebook documenting lab procedures, problem-solving, data collection, graphing,
analysis, and future recommendations
Learning Objectives:
Students will be able to:
• create a poster describing the mechanism and effects of gene expression regulation on
cells.
• perform an experiment where they induce expression of a gene with an environmental
factor and observe phenotypic change.
• predict the effect of an environmental factor on gene expression and interpret their
observations.
• observe differences in mammalian cell types and propose causes for different
morphology and function.
• interpret a gene expression heat map to predict the tissue type represented.
Skills to be developed
• observation
• hypothesizing
• experimental design
• microscopy
• performing genetic transformation
• note-making
• presenting scientific information
• analyzing graphical representations of data
• laboratory notebook record-keeping
GENA Partnership Planning Worksheet
Possible Student Misconceptions:
• Because all cells in an organism contain the same genetic information, they have the
same genes expressed.
• Genetic mutations are the main mechanism for altering phenotype.
• The central dogma of molecular biology adequately explains the relationship between
genotype and phenotype.
Vocabulary focus:
• promoter
• gene
• transcription factor
• RNA polymerase
• repressor
• up/downregulate
• gene expression
• differential gene expression
• development
• genome
• chromatin
• environmental factor
• splicing*
• enhancer*
Curriculum sourcing:
Most of the curriculum will be self-designed. We will use the Amgen-Bruce Wallace
transformation materials for the lab.
Task analysis:
• central dogma
• principles of transformation
• general knowledge of molecular genetics
Day 1
Learning Objective:
SWBAT explain how gene expression affects phenotype.
Assessment: Administer pre-assessment quiz
Engage:
Show video of breast cancer cells dividing. Ask students: “What do you think makes these cells
different from non-cancerous breast cells? Is the DNA in all of the cells the same? Different?” If
students say the DNA is different, ask them: “How different is the cancer cells’ DNA from the
normal cells? 0.01%, 10%, 99%?”
2
GENA Partnership Planning Worksheet
Show picture of tan lines on feet. Ask students: “What makes the cells of the lighter color skin
different from the darker colored skin? Is the DNA in all of the cells the same?”
Explore:
Define cell differentiation for the students:
“A normal process in development in which cells become structurally and functionally different
from one another and develop a mature phenotype — for example, fat, muscle and liver cells.”
Nature Magazine
Write the following questions on the board: “If all of the DNA in all of an individual’s cells are
the same, how is it possible to have different cell types? How is it possible that the cells lining
your stomach and the cells of your retina (eyeball) have identical DNA in their nuclei?”
Divide the class into pairs of students. Ask them to talk in their pair for 2 minutes about theses
question. Pass out two post-its (one yellow, one green) to each pair and ask them to write one
thing they are sure of on the green post-it and a question they have on the yellow post-it.
Create a large poster and write “Cell Differentiation” at the top. Underneath, create 3 columns:
“Know”, “Want to Know”, “Learned” (KWL). Then have each group place the green post-its
underneath “Know” and the yellow underneath “Want to Know” on the large poster. Read the
ideas aloud to the class and refrain from commenting on the accuracy of their ideas. Post the
KWL chart in the classroom and it up for the duration of the unit.
Explain:
Read the short essay “Gene Expression” from the University of Utah. Each student writes a
short summary paragraph in his or her notebook. Have students exchange notebooks with a
neighbor and read the other person’s paragraph. Call on students to identify ideas in the other
student’s notebook that they also thought were important. Create a list on the board of consensus
ideas. Ask students to find ideas in the other students’ notebooks that are confusing or
inaccurate and discuss as a whole group. At this time, make sure that any misconceptions are
clarified.
Assessment:
Exit slip: “Choose two cell types from the same individual organism. Describe two things that
those cells have in common and two differences between them.”
Homework:
Students need to create a data table in their notebook for the microscopy lab the following day.
Each student will look at 3 tissue types. It must contain areas that will be used to:
• write the name of the sample
• draw the field of view in the microscope
• describe the appearance of the cells in several sentences
Day 2
Learning Objective:
SWBAT use a microscope to view prepared slides of various tissue types.
3
GENA Partnership Planning Worksheet
SWBAT draw a representation of various tissue types.
SWBAT explain the role of DNA in the differences between the various cell types.
Engage:
Show students the following video of a pulsing myocyte. For their warm up have them talk with
a partner about what makes that myocyte different from a cell on the back of their hand. Write a
three-sentence summary for their warm up including the terms “development”, “gene
expression” and “DNA”.
Explore:
Ensure that groups of students have microscopes and at least three slides of different tissue types.
Ask the students to look at the slides and choose a field that is interesting to them (for any
reason). Choose three different tissue types to record in their notebook. For each type, all
students must:
• write the name of the sample
• draw the field of view in the microscope
• describe the appearance of the cells in several sentences
This will require that they look, try to remember as much as possible and draw while the next
student is looking at the same field. They will need to take turns for each student to complete the
assignment.
Explain:
Each group should come up to the document camera and choose one notebook to show to the
other students about one of their 3 samples. They should tell the whole class about what tissue
type they looked at and what they found interesting about it. How many different types of cells
were present? How could you tell which cells were a different type? Do the cells look exactly as
they would in the body? What differences might you expect to find between the slides and living
cells? Allow each group about 3 minutes to share their findings.
Elaborate:
Students return to their own seats and choose one adult human cell type (Wikipedia has
comprehensive list of cell types to choose from). Their assignment is to create a poster
describing that cell type. They may use the internet for resources, as well as classroom books,
but all sources must be cited. This poster can be finished as homework.
Assessment:
Have the students answer the following question on an exit slip: “What most interested you
about your cell type? How does the DNA of the cell lead to its interesting properties?”
Day 3
Learning Objective:
SWBAT explain the role of gene expression in skin pigmentation.
SWBAT perform a virtual microarray experiment.
SWBAT describe one method for measuring gene expression
4
GENA Partnership Planning Worksheet
Engage:
Students will write a three-sentence answer to the following question, using the terms “gene
expression” and “environmental factor” in their response: “What allows some skin to turn
browner in the summer?” Discuss their answers as a whole class.
Explore:
Show the video “Personal Genome Project”. After the video, have the students answer the
following questions in pairs: “Would you participate in the Personal Genome Project? Why did
the sequencing of ‘the human genome’ not tell us every secret of how our bodies work?”
Explain:
Students take notes from Dr. Rana’s Powerpoint presentation and write a summary of their
learning.
Elaborate:
Students complete the DNA Microarray Virtual Lab and write a one paragraph abstract of their
findings, including the limitations of the technology.
Assessment:
Have the students write a two-sentence explanation of microarray technology, including its
primary functions and at least one limitation on an exit slip.
Days 4-7
Learning Objective:
SWBAT describe how an inducible promoter works.
SWBAT hypothesize the result of bacterial transformation and controls.
Engage:
Students know about fluorescent proteins from prior transformation experiments. Ask them to
imagine a way to turn on a gene.
Explore:
Students watch this video about the lac operon. You may want to stop the video at 2:00 to
prevent information overload. Have a short class conversation about how the operon works. This
will help them start to think about environmental factors and inducible promoters. Have students
come up to the board and draw the action of the repressor when lactose is/ is not present.
Explain:
Show Powerpoint presentation for the Transformation lab. Students take Cornell notes in their
notebook and write the full protocol in their lab notebook.
Elaborate:
Students complete the lab as directed in the attachment (very detailed information there).
Students complete analysis and conclusion questions as they proceed.
5
GENA Partnership Planning Worksheet
Assessment:
Students complete a poster, powerpoint or other presentation to explain the regulation of gene
expression to a 10th or 7th grade science class, depending on who is available to listen. Students
may work in groups or independently. The students may direct their own project, but it must
contain the following information:
• A definition of gene expression
• An example of a situation where differential gene expression leads to a phenotype
• How a reduction in mRNA transcript affects protein levels
• How protein levels relate to a phenotype
Students will present their projects first to the class. Students will then be asked to anonymously
vote if the presentation should go to other classes, using the following scoring guide:
Category
Agree Unsure Disagree
th
th
Gene Expression is defined clearly in terms a 7 /10 grader can
3
2
1
understand
An interesting example of gene expression is given and explained
3
2
1
clearly.
The effect of gene expression on mRNA levels and phenotype are
3
2
1
clearly explained.
The presentation is clean, neat and free of errors, including
3
2
1
spelling and grammar.
Presenters were professional, spoke clearly and kept your
3
2
1
attention.
Any presentation with an average score of 12 or higher will be excused from class at a later date
to present to another classroom, unless the teacher deems it inappropriate.
Final Assessment:
Post-lesson quiz.
6
Form: A
Gene Expression
Multiple Choice
Identify the choice that best completes the statement or answers the question.
1. Gene regulation in eukaryotes
a. usually involves operons.
b. is simpler than in prokaryotes.
c. allows for cell specialization.
d. includes the action of an operator region.
2. In eukaryotes,
a. transcription takes place in the cytoplasm, and translation takes place in the nucleus.
b. transcription takes place in the nucleus, and translation takes place in the cytoplasm.
c. transcription and translation both take place in the nucleus.
d. transcription and translation both take place in the cytoplasm.
Microarray Chips
Chip A
Chip B
Chip C
3. Look at the diagram of the microarray chips above and choose the answer that best describes the data.
a. The RNA on chips A and C come from the same tissue type.
b. Chip B is from a mutant organism.
c. The RNA on chips A and B come from the same tissue type.
d. All of the spots on the plate hybridized with probes.
4. Which is involved with the regulation of eukaryotic genes?
a. operon
b. DNA polymerase
c. promoter
d. operator
5. You have just spent a long day at the beach and your skin is a darker shade. What caused this change in
color?
a. The UV rays damaged your DNA which c. Environmental exposure altered the
mutated a gene, causing your skin to
expression of genes in your brain,
darken immediately.
causing your neurons to instruct skin
color to change.
b. Environmental exposure altered the
d. The heat from the sun denatured
expression of genes in the
proteins in your skin, causing it to look
pigment-producing cells.
darker.
1
Form: A
6. What is regulated gene expression?
a. A process by which microarrays detect which cells are producing which proteins
b. The cells ability to turn “on” and “off” genes at particular times
c. A VNTR amplification protocol
d. A method for blotting DNA fragments onto a positively charged membrane
7. About how much of our DNA encodes the instructions for building proteins?
a. 2 percent
b. 10 percent
c. 50 percent
d. 100 percent
Figure 13–4
8. The basic body structure of the fly in Figure 13–4 is determined by
a. repressor genes.
b. developmental genes expressed in specific patterns.
c. inversion mutations.
d. frameshift mutations.
9. Specialized cells regulate the expression of genes because they
a. do not want the genes to become worn out.
b. cannot control the translation of proteins.
c. do not carry the complete genetic code in their nuclei.
d. do not need the proteins that are specified by certain genes.
2
Form: A
10. What is produced during transcription?
a. RNA molecules
b. DNA molecules
c. RNA polymerase
d. proteins
11. What regulates the expression of most eukaryotic genes?
a. miRNA
b. transcription factors
c. dicer enzymes
d. silencing complexes
12. A promoter is a
a. binding site for DNA polymerase.
b. binding site for RNA polymerase.
c. start signal for replication.
d. stop signal for transcription.
Short Answer
13. Describe how a cell in the skin of your hand and a cell in your eyeball are different when they contain the
exact same DNA sequence. Please use the following terms in your answer: expression, genes, development,
mutation.
3
ID: A
Gene Expression
Answer Section
MULTIPLE CHOICE
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
ANS:
ANS:
ANS:
ANS:
ANS:
ANS:
ANS:
ANS:
ANS:
ANS:
ANS:
ANS:
C
B
D
C
B
B
A
B
D
A
B
B
STA: CA.BIO.1.c
STA: CA.BIO.1.d
STA: CA.BIO.1.c
STA:
STA:
STA:
STA:
STA:
STA:
CA.BIO.5.c
CA.BIO.4.d
CA.BIO.1.c
CA.BIO.5.a | CA.BIO.5.b
CA.BIO.1.c
CA.BIO.4.a
SHORT ANSWER
13. ANS:
3: Due to differential gene expression, developmental cues lead to changes in g.e., not due to mutations or
change in DNA sequence.
2: Gene expression plus one other from above 2 of the three above
1: Due differential gene expression
0: No mention of gene expression or major misconception is present.
1
8/31/2010
What makes cells from the same individual look different?
GENE EXPRESSION
Brinda K. Rana, Ph.D.
Assistant Professor
UCSD School of Medicine
Stem Cells
Liver Cells
Red Blood Cells
Cartilage Cells
What makes cells from the same individual look different?
Development: Expression Patterns of Genes Change throughout Your Lifetime
Stem Cells
Liver Cells
Red Blood Cells
Baby Pigpen
Cartilage Cells
Teenager Pigpen
DNA sequence in each cell is the same, but different cell types have different
“GENE EXPRESSION PATTERNS”
Development of Fly
EGG
Environment during Life and as an Embryo
Can Influence Gene Expression Patterns
EMBRYO
These mice are genetically identical (SAME DNA SEQUENCE).
They come from 4 pairs of genetically identical parent mice.
LARVAE
Their moms had different diets which influenced their fur color.
1
8/31/2010
Gene expression patterns can be used to diagnose disease
What happens when normal gene expression patterns are changed?
Example:
Suppose there are two types of cancers that require different treatments,
but it is hard to tell the two cancers apart by looking at the tumor cells.
Example: “Antennapedia “
As a molecular biologist, you devise a genomic test to determine the type
of cancer.
Gene expression patterns in tumors from two cancer types
Type 1 Type 2
Gene A
X
Gene B
X
Gene C
Gene D
A mutation in the regulatory region of HOX gene causes legs to grow
where there should be antenna
X
Gene E
X
Gene F
X
Suppose you have a group of kittens who are sick with either type 1 or type 2 cancer.
Suppose you have a group of kittens who are sick with either type 1 or type 2 cancer.
Conduct gene expression profiles on the kittens to determine which cancer kitten has.
Conduct gene expression profiles on the kittens to determine which cancer kitten has.
Gene A
X
X
X
X
Gene B
X
X
X
X
X
X
X
X
Gene C
Gene D
Gene E
X
Gene F
X
X
X
X
X
X
X
Type 1
Suppose you have a group of kittens who are sick with either type 1 or type 2 cancer.
Type 2
Molecular Biology of Gene Expression:
How Fireflies Light Up their Tail
Conduct gene expression profiles on the kittens to determine which cancer kitten has.
Gene A
X
X
X
X
Gene B
X
X
X
X
X
X
X
X
Gene C
Gene D
Gene E
X
Gene F
X
X
X
X
X
X
X
Type 1
Treatment alpha
luciferase
enzyme
Oxygen + Luciferin Æ Oxyluciferin
Type 2
Treatment beta
Adapted from University of Utah Genetic Science Learning Center
2
8/31/2010
Molecular Biology of Gene Expression:
How Fireflies Light Up their Tail
nucleus
luciferase
enzyme
Oxygen + Luciferin Æ Oxyluciferin
Adapted from University of Utah Genetic Science Learning Center
Adapted from University of Utah Genetic Science Learning Center
DNA
RNA Polymerase
LUC Gene
3
8/31/2010
Ribosome = Translator
“Good Afternoon”
4
8/31/2010
Review of Concepts: Process of Gene Expression
Review of Concepts
Promoter &
transcription factors
Environmental factors
Differential gene expression
Gene expression changes through development
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Brinda K. Rana
Reflection on unit:
California State Standards for high school Biology requires that students understand the
following concepts: (1) “Genes are a set of instructions encoded in the DNA sequence of each
organism that specify the sequence of amino acids in proteins characteristic of that organism”;
(2) “The genetic composition of cells can be altered by incorporation of exogenous DNA into the
cells”; and that (3) “Mutation and sexual reproduction lead to genetic variation in a population.”
High Schools in San Diego County have incorporated DNA transformation laboratories and
curricula on genetic diversity and human mutation to demonstrate these important concepts.
However, the emphasis on DNA mutation and the “central dogma” seems to be causing
misconceptions about the important role of gene expression in human disease, development,
population variation, and cell differentiation. I came into the GENA project wanting to provide
students with a curriculum to dispel these misconceptions and provide them with an
understanding that gene expression is a complex and changing process in which the
environment interacts with the genome to regulate the synthesis of a functional gene product.
Fortunately, through GENA, I was matched with a teacher who, prior to entering a career
in teaching, had worked in industry conducting gene expression assays and had graduate
experience in molecular biology. In addition, through other teacher development programs,
Sara brought a background in developing laboratory activities as well as materials for activities.
Sara encouraged developing a curriculum that directly built upon a curriculum she and her
colleagues have already established in their classrooms--DNA transformation of mutated
fluorescent proteins to demonstrate the “central dogma”. The students’ prior experience with
DNA transformation techniques made it possible for us to carry out our gene expression
curriculum efficiently without expending time to develop basic laboratory skills. Thus we were
able to focus our time on gene expression concepts.
I expected that the students would grasp only a small portion of my introductory lecture.
However, midway through my first lecture, I could tell that the students were grasping the
majority of the concepts I was presenting. Thus, the time spent with Sara in understanding the
concepts the students had a firm grasp on and the time spent with both Sara and other teachers
at the GENA workshop discussing causes of misconceptions was essential. I also clearly
observed that building on the established curriculum provided the students an opportunity to ask
new questions on concepts they were already comfortable with. This increased the
effectiveness of student learning.
Reflections on obstacles faced in the process:
Resources: San Diego High School is the oldest high school in the city of San Diego and one of
over 40 high schools in San Diego County. This inner-city school has a large and diverse
population (about 3000 students). The socio-economic background of the students and the
neighboring community is an obstacle for student achievement. Resources are visibly limited at
this school and parent involvement is negligible. San Diego High is fortunate to have a handful
of extremely hard working teachers such as my teacher partner, Sara Dozier, who works
seemingly non-stop to overcome these obstacles and obtain resources to teach curriculum
which many other schools in the county take for granted. We loaned Sara a portable autoclave
for her classroom to make reagents and agar plates for this and other projects. Sara has since
obtained a grant to purchase equipment and her own autoclave. Funding for transportation for
field trips is difficult to obtain. UCSD is 16 miles from San Diego High School and students will
need to be transported by bus to our campus.
Time restraints. Time restraints caused us to truncate some of our plans during the first pilot. I
was surprised to learn that Sara has her students for only one semester, so time is limited to
incorporate this one week curriculum. We were unable to carry out the curriculum the second
semester due to school district mandated testing resulting in a shortened semester. I was also
unable to incorporate a lecture on gene expression technology (e.g. microarray platforms, chips)
during the first pilot of the curriculum. In the Fall semester, we will incorporate the technology
lecture and include a pre- and post- assessment. I would also like to bring the students to
campus to tour our gene expression facilities if resources and time permits.
Thoughts on Dissemination, Sustainability, and Follow-up: I learned through the GENA process
that there exists a plethora of online curriculum resources available for teachers on just about
every topic in science. How teachers are able to go through all these resources and obtain the
expertise needed to effectively carry out the activities? Will this limit how far reaching Sara and
my curriculum will be? Other concerns are resource restraints within San Diego High School to
carry out our curriculum in future years and recruiting other teachers at Sara’s high school to
incorporate our curriculum in inner-city schools such as Sara’s. I also wonder how much
influence our curriculum will have on students who come from backgrounds where higher
education is not encouraged.
Reflections on Participation in GENA
My partnership with a high school genetics teacher gave me insight into the background
that undergraduate students enter the university with. This will enhance my ability to teach
incoming undergraduate students. I have also never been trained formally in curriculum
development. I value the opportunity to learn GENA’s 5E Model and apply this model. Pairing
with a well trained and highly motivated teacher enhanced my experience.
It was a boost that Sara’s students were extremely receptive of my visit and attentive
during my lecture. Sara and I will continue to access the impact of our curriculum on student
learning in coming years. However, what may be more important than learning concepts in
gene expression is that these students now have a new pathway to access scientists and the
University of California. This is important as the majority of these students come from families
with low income and limited educational background. Does GENA or ASHG have a mechanism
to continue to engage GENA students in genetics through outreach programs? Can the GENA
project be publicized in local media so that students can be acknowledged for their participation
in the GENA pilot projects?
GENA Project
Reflection
Sara Dozier
Working this year with Dr. Rana was an incredibly helpful experience. She is a
unique scientist in that she excels within her field but has a deep respect for the art
of teaching. This shows in her relationships with the undergraduates she works
with and translates almost seamlessly to the high school classroom. In our unit of
study we created lessons that would help students understand how gene expression
can affect phenotype and how it is studied and measured by scientists in various
fields of research.
Dr. Rana suggested that we teach the students about microarray technology, a
powerful tool for studying global gene expression changes. At first, I was hesitant to
attempt to teach this to my students because I thought it would be conceptually too
difficult for them. Dr. Rana found a way, in her lecture slides, to make the ideas
accessible to the students. I appreciated having the opportunity to work with a
scientist who challenged me to challenge my students.
The main problem we faced was one of time. It was very difficult to find
opportunities to teach the lessons and have Dr. Rana present in the classroom. We
hope to continue our partnership next year. To avoid the scheduling difficulties, we
have already scheduled days for her to come to the classroom and I have allotted
more time to teach the unit.