Be a LifeSaver: Detection is the Key to a Cure
By
Lynne Coté
Mountain View High School (MUSD)
10th-11th graders, Biomedical Fundamentals
In partial fulfillment of the requirements for
TTE596c
Summer 2012
SCENARIO
When you here the word “Cancer” what feelings do you experience? The thought of you or someone
you know having cancer can be devastating. According to the American Cancer Society, half of all
men and one-third of all women in the US will develop cancer during their lifetimes. This means the
likelihood of one of the 100 plus forms cancer directly or indirectly affecting your life is very high.
Knowledge could be the key to survival.
In normal cells damage to DNA is either repaired or the cell dies. In cancerous cells this regulation
does not occur and the cell continues to divide uncontrollably. Normal cells are polite and will stop
multiplying when they touch another cell. Cancer cells are rude and will continue dividing to form
tumors. Sometimes the cancer cells migrate (metastasize) to other areas of the body and forms new
tumors comprised of cloned cells from the original cancer cell.
Today, millions of people are living with cancer or have had cancer. The risk of developing many
types of cancer can be reduced by changes in a person’s lifestyle, for example, by staying away from
tobacco, limiting time in the sun, being physically active, and healthy eating. There are also screening
tests that can be done for some types of cancers so they can be found as early as possible – while
they are small and before they have spread. In general, the earlier a cancer is found and treated, the
better the chances are for living for many years. But is the same treatment the best for everyone?
You are a scientist that works in the Research and Development department at a well-known
biotechnology business known for developing diagnostic tools for various cancers. A person you love
has been diagnosed with cancer and comes to you for advice on what type of treatment they should
undergo. You are charged with developing a diagnostic tool (probes and antibodies) to determine the
characteristics of your relative’s cancer so that you can suggest what the best treatments they should
consider.
Images?
Stage 1 – Desired Results
Established Goals
Transfer
 Student will be able to (SWBAT) use bioinformatics resources
Arizona Bioscience CTE
(HUGO, NCBI, UCSC) to design probes and antibodies to enable
Standards & MC:
a diagnosis and recommendation of a possible treatment of a
10.0 Demonstrate
patient.
understanding and knowledge
 Student will be able to analyze cells using a microscope to
of cell biology techniques
evaluate characteristics involving presence of gene, mRNA and
10.1 Isolate and characterize cell
protein production.
lines
10.4 Use microscopes
10.5 Perform cytological tests,
Meaning
i.e. sectioning and staining
Understandings
Essential Questions
14.0 Demonstrate use of
 Bioinformatics involves using How do structures of biologically
bioinformatics resources
online databases and tools to important molecules (i.e. nucleic
14.1 Identify databases for
analyze nucleotide sequences, acids-DNA & RNA, proteins)
sequence analysis (NCBI)
account for their function?
RNA, and proteins.
14.2 Utilize electronic
 Nucleotide sequences code for
databases/websites (NCBI)
mRNA and protein.
14.3 Identify unknown sequences  Probes can be designed to
14.4 Recognize relationships
target (recognize) specific
between sequences
nucleotide sequences and
15.0 Demonstrate
RNA.
understanding and knowledge  Probes and antibodies are
of nucleic acid techniques
used as diagnostic tools for
15.1 Detect specific nucleic acid
specific cancers.
sequences
 Probes and antibodies used in
15.8 Use sequence database
identifying nucleotide
sequences are fluorescently
Arizona High School Life
labeled to visually be seen
Science Standards:
through a microscope.
S4C2PO1 Analyze the
relationships among nucleic acids
(DNA, RNA), genes, and
Acquisition
chromosomes

S4C2PO2 Describe the molecular
basis of heredity, in viruses and
living things, including DNA
replication and protein synthesis 


Student will know that unique 
nucleotide sequences of ~100
bp are needed to design a
probe.
Student will know that
nucleotide sequences and

mRNA are recognized by
probes and proteins by
antibodies.
Student will know “Molecular
Biology Central Dogma”
(DNARNAProtein) and
variations that occur.
Student will know how cell’s
communicate.
Student will use the
appropriate bioinformatics
resource (HUGO, NCBI,
UCSC) to accomplish a certain
task.
Students will analyze slides
and distinguish between
cancerous and noncancerous
cells based on qualitative
microscopic observations (# of
gene copies, overexpressed
RNA, excess protein
production).
Stage 2 - Assessments
Performance Task (in GRASPS format)
Goal:
 Your challenge is to develop diagnostic probes and antibodies to help a relative and their doctor
determine the specific form of cancer they have and what treatment they should be undergoing.
Role:
 You are a scientist in the Research and Development lab of a major biotechnology company.
Audience:
 Your need to inform your relative and their doctor as to the genetic and molecular basis of the
cancer.
Situation:
 The challenge involves using bioinformatics to design diagnostic tools in the form of probes and
antibodies.
Product, Performance, and Purpose:
 You will develop probes and antibodies specific to the DNA, mRNA, and proteins that are being
over expressed by you relative due to their cancer.
Standards and Criteria for Success:
 Your product must meet the following standards:
o Use HUGO to determine the official name of the gene of interest
o Use a genome browser, NCBI or UCSC, to determine the gene sequence
o Determine a probe specific to the gene of interest and produce a FASTA result sheet
verifying that the probe sequence is unique only to the gene of interest
o Research and determine a possible protocol of treatment best suited for your relative.
Other Evidence: (quizzes, tests, prompts, work samples, labs, etc.)
 Labs:
o Using HUGO to Find Official Gene Name
o Using NCBI or UCSC to Isolate the Gene
o Designing a Probe for Detection of the Gene
 Prompts:
o Why, other than determining if a gene is present, is gene detection so important in
determining a form of treatment for patients?
o Why is it important to determine the official name (acronym) of a gene?
o Which gene browser did you prefer? Why?
o What are the important aspects to keep in mind when designing a probe? How can you
increase probe specificity?
Student Self-Assessment and Reflection
 Entries in Lab Books
 Reflections in Journals
 Peer Evaluations of Probes
UNIT MAP
Stage 3 – Learning Plan
1. Begin with the scenario and pose the question, “What would you
do to save a loved one?” to hook the students into the
importance of research. H
2. Introduce the students to the Essential Question and discuss
the unit performance tasks and rubric. W
3. Ask students brainstorm three questions: (1) What are the key
concepts of the Central Dogma of Molecular Biology and how
do they interact with each other? (2) What is Cancer? (3) What
is Bioinformatics? Their responses will act as a pre-assessment
of prior knowledge and potential misconceptions. R, E2
4. Students view, “What is Cancer?”, video and select one of the
suggested cancer readings to review. Students complete a
journal entry summarizing video and reading they selected. In
the entry they should include what they learned and what
questions they still have about cancer. E
5. Class discusses results of previous brainstorming activity and
reflects on revisions that should be made to clear up any
misconceptions. Teacher addresses misconceptions not
resolved by students’ reflection. E, R, E2
6. Students think of someone they actually knew that has or had
cancer. The then complete the HUGO online activity for
example gene (HER2) and for the gene they researched to get
the official name and acronym. Students can follow written
instructions or open video and follow along as they are working
through the process. E, T
7. Next students will complete the Finding a Sequence Using
NCBI or UCSC for their gene of interest. Students can follow
written instructions or open video and follow along as they are
working through the process. E, T
8. Students perform a BLAST or BLAT with the FASTA form
created for their gene. E
9. Students analyze genes and determine the best probes based
on BLAST/BLAT following written instructions. E
10. Students peer-review another student’s work on Steps 7-9 and
discuss areas of improvement if needed. E2
11. Students repeat steps 7-10 for RNA. E
12. Students reflect back on DNA and RNA sequences and write
relationships between the two in their journals. E, R
13. Students show printout of and explain their findings to the
teacher. (Note: Teacher collects and reviews students’ results
of HUGO, Finding a Sequence Using NCBI or UCSC,
BLAST/BLAT, and probe design. Based on student’s
explanation, teacher clears up misunderstandings or gaps on a
student-by-student basis. E2
14. Students analyze teacher-prepared slides of HER2+ cancer
slides for DNA and RNA and write in their journal how the two
Pre-Assessments
What pre-assessments will you use to
check student’s prior knowledge, skill
levels, and potential misconceptions?



Prompt: What are the key concepts
of the Central Dogma of Molecular
Biology?
Prompt: What is Cancer?
Prompt: What is Bioinformatics?
Progress Monitoring
How will you monitor students’ progress
toward acquisition, meaning, and
transfer, during lesson events?




Student progress will be monitored
through:
Verbal questioning of students
throughout activities.
Products of bioinformatics labs
Analysis of tissue slides.
slides compare and what that tells about the relationship
between DNA and RNA. (Teacher checks journal entries and
determines basis of class discussion to follow.) E, R, E2
15. Class discussion of alterations to Central Dogma that was
presented in a simplified form in previous year. R
16. Students are asked to reflect and answer the question, If a
treatment is found of a type of cancer, should everyone with
that cancer get that treatment? Why or Why not? Student
writes reflection in their journal. E, R
17. Class discussion of why personalized medicine comes into
play in this case and why knowledge is power. E
What are potential rough spots and
student misunderstandings?
Common genetics misunderstandings
include the following ideas:
 Every aspect of the biology of an
organism can be predicted from its
genes.
o It is much more complicated
involving expression of genes
and regulatory pathways.
 The relationship between genes and
proteins as one-gene codes for one
protein.
o In actuality, one gene can
code for more than one
protein.
 Genes are uninterrupted sections of
DNA that only code for a single
protein.
o This negates the
understanding of introns and
exons.
 The sole function of genes is to code
for proteins, with the non-coding
remainder being "junk DNA. "
o However, it now appears that,
although protein-coding DNA
makes up barely 2% of the
human genome, about 80% of
the bases in the genome may
be being expressed, so the
term "junk DNA" may be a
misnomer.
 The Central Dogma (DNA→ RNA→
Protein) no longer is the rule.
o Genes → Gene expression →
Proteins → Metabolic
pathways → Sub-cellular
structures → Cells → Tissues
→ Organs → Organisms
o Epigenetics also comes into
play.
How will students get the feedback they
need?
 Verbal Feedback (From Teacher &
Peers)
 Written Feedback on Assessed Labs
Activities
• Are all three types of goals (acquisition, meaning, and transfer) addressed in the learning plan? Yes
• Does the learning plan reflect principles of learning and best practices? Yes
• Is there tight alignment with Stages 1 and 2? Yes
• Is the plan likely to be engaging and effective for all students? I hope so.
APPENDICES
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3D Medical Animation-What is Cancer?
Hallmarks of Cancer
Hallmarks of Cancer: The Next Generation
Roots of Cancer
Understanding Cancer Video
HUGO Instructions
HUGO Instructional Video
Finding a Sequence Using NCBI & UCSC Instructions
Finding a Sequence Using NCBI & UCSC Video
DNA Probe Design Instructions
Bioinformatics Mindmap
Unit Rubric