Lesson Plan Template
Name of Lesson/Unit: DNA Barcoding
Grade Level: 10-12
Prepared by:
Section 1: Lesson Summary
Topic: Evidence of molecular heredity and evolution
NGSS Performance Expectation: HS-LS3-2: Make and defend a claim based on evidence that
inheritable genetic variation may result from 1) new genetic combinations from meiosis, 2) errors
in replication, or 3) mutations.
Crosscutting Concept: Cause and Effect – Empirical evidence is required to differentiate between
cause and correlation and make claims about specific causes and effects.
Engineering Practices: Analyzing and interpreting Data – formulating, refining, and evaluating
empirically testable questions and design problems using models and simulations.
Common Core State Standards (Reading): “Barcode of Life” by M. Stoeckle and P. Hebert,
Scientific American, October, 2008, pp. 82-88. RST.11-12.1
Cite specific textual evidence to support analysis of science and technical texts, attending to
important distinctions the author makes and to any gaps or inconsistencies in the account.
Common Core State Standards (Writing): WHST.9-12.1 Write arguments focused on
discipline-specific content. Students will prepare a written defense of research communicating
the analysis and conclusions of their research.
Current CA Science Standards: Students know how mutations in the DNA sequence of a gene
may or may not affect the expression of the gene or the sequence of amino acids in an encoded
protein. Students know new mutations are constantly being generated in a gene pool.
Objective of the Lesson or Unit: Students will observe, record and analyze molecular evolution
and predict semiquantitatively how this may affect phenotype (e.g., DNA nucleotide differences
and amino acid changes in the gene product).
How is this objective relevant to students? Students will be completing a research project and
writing a research paper for publication. Students will be participating in a worldwide scientific
initiative to barcode 5 million specimens representing 500,000 different species and make the
data available to the scientific community in the International Barcode of Life (iBOL) database.
Culminating Assessment (How will you know students have met the Performance Expectation?)
Describe the assessment and attach a copy. Students will produce a research paper for
publication. Students will present a defense of their research to the Science Magnet faculty and
invited scientists.
Lesson Plan Template
What has been taught in my class to prepare students for this topic? DNA replication,
transcription, translation, protein structure and function, cellular respiration, mechanisms of
evolution, natural selection, experimental approaches and techniques used in molecular life
science
Description of the Lesson/Unit (Use the following Table)
With 5 E and How
Short description of activity
People Learn in Mind!
Engage
Students join the iBOL DNA
barcoding scientific initiative
Explore
Students collect specimens,
extract total DNA, amplify
COI gene, purify amplicon by
spin column chromatography,
use automated DNA
sequencing to determine 650
bp vertebrate COI barcode
amplicon
Explain
Students will analyze DNA
barcodes of specimens: create
phylogenetic tree, identify
intraspecific and interspecific
nucleotide differences of
specimen barcodes; identify
codon changes, determine
nucleotide position within the
codon, determine amino acid
Purpose/Intention for the activity or
Key Learning
 How does this activity build
student knowledge and skills
towards meeting the
Performance Expectation?
 Identify at least 1 Practice
Students discover the value of species
identification and taxonomy in order to
preserve and utilize the biodiversity of
the biosphere and how they can
contribute to the scientific community
through DNA barcoding; students
develop an understanding of how
molecular evolution contributes to
speciation
Students carry out molecular life
science protocols to determine the
DNA barcodes of their specimens;
students are motivated to understand
the concepts of DNA replication,
transcription, translation, oxidative
phosphorylation and the techniques of
molecular life science (nucleic acid
isolation and purification, polymerase
chain reaction PCR and DNA
sequencing) which are relevant to their
research
Students gain an in depth
understanding of the expression of
genetic material, the nature of
evolutionary mutations and their
effects on gene products, the molecular
basis for speciation as depicted in a
phylogenetic tree, and the power of
computational biology in analyzing
large amounts of data; students create
Lesson Plan Template
Elaborate
Evaluate
produced in the gene product,
quantify these changes, and
determine their effect on the
gene product
Students create a scientific
research paper for publication
in which they communicate
the findings of their research
Students will present a defense
of their research to the Science
magnet faculty and invited
scientists
specimen pages and sequence pages
from their research on the eBOL
database which appears on NCBI after
teacher and scientist vetting.
Students analyze and incorporate
primary resources in communicating
their analyses and conclusions of their
research
Defending their research in a high
stakes situation will allow both the
students and the teacher to assess the
extent to which students have
developed in depth understanding of
content, that students reached logical
and evidence based conclusions, and
the effectiveness of communicating
their findings with the academic and
scientific community
Section 2: Laboratory/ Hands-on Lesson
Content Objective: Students will use bioinformatics to identify mutations in DNA barcodes of
rockfish species as evidence of evolution, and will analyze the effect of mutations on the gene
product; students will construct a phylogenetic tree illustrating the evolutionary relationships
among the DNA barcoding specimens
Language Objective: Students will become fluent in the use of relevant biological terms related
to DNA barcoding and their research.
Assessment: How will I know students met the objective?
Students will prepare a scientific manuscript for publication which will be submitted to an
appropriate journal (National High School Journal of Science, Journal of Experimental
Secondary Science, Journal of Youths in Science, Torrey Pines Falconium Journal, etc.)
Rubric:
Assessment criteria
1. Students follow the format for the journal to which they submit their manuscript.
2. Students introduce the research topic and provide sufficient background information for
general understanding.
3. Students clearly state the questions and/or hypotheses being addressed in the research.
4. Students describe the experimental procedures utilized to address the questions/hypotheses.
5. Students present the data in appropriate tables.
6. Students use appropriate analytical and statistical methods to interpret data.
7. Students thoroughly discuss and explain research results, relating them to current scientific
theories and applications.
Lesson Plan Template
Description of lesson: Bioinformatics of DNA barcodes to identify mutations and analyze their
effects on the gene product, COI.
Students use BLAST to align DNA barcodes of class specimens to identify nucleotide changes;
students quantify the codon positions in which they occur and the type of base substitution
(A→G, C→T, etc.); students determine the types of amino acid changes that occur due to
nucleotide changes; students identify the locations of amino acid changes in the protein sequence
of COI
Time required for the lesson: 2 hour introduction of bioinformatics tools (BLAST, nucleotide
changes, open reading frame (ORF), vertebrate mitochondrial genetic code for sequence
translation; 2 hours of student analysis; 2 hours of homework to communicate findings for
manuscript
Materials/ Preparation needed: DNA barcode sequences on BOLD-SDP
(www.boldsystems.org), computers with Excel
Description of Student
Task (each step)
Time
Needed for
Students to
complete
each Task
Use BLAST to align
class DNA barcodes;
use aligned sequences
to identify and tabulate
nucleotide differences
1 hr. class, 1 First 15 minutes: have students
hr.
attempt to manually align DNA
homework
barcode sequences
Introduce power of
computational biology to align
sequences instantaneously (15
min)
Have students select DNA
barcodes from BOLD-SDP and
align (15 min)
Have students brainstorm
efficient strategies to tabulate
nucleotide changes (15 min):
check for understanding.
1 hr. class, 1 These concepts have been
hr.
covered previously in a research
homework
project to clone and express a
Quantify the different
types of base
substitutions and the
Teacher Notes
(Include strategies/questions to
check for understanding)
Accommodation/Mo
dification for
Student Access and
Extension (i.e.
strategies for EL and
extensions for
GATE)
EL: check for
understanding of
relevant vocabulary
GATE: addition of
statistical analysis of
data to determine pvalues
EL: check for
understanding of
relevant vocabulary
Lesson Plan Template
codon positions in
which they occur;
identify the open
reading frame (ORF) in
order to identify the
amino acid changes
produced by the
nucleotide changes
Analyze the frequency
of changes in different
codon locations and
open up a discussion to
interpret the findings;
analyze the types of
nucleotide changes and
whether they produce a
change in the amino
acid of the gene
product; open up a
discussion of the types
of amino acid changes
which occur and where
in the gene product they
occur
gene and then isolate the gene
product; review, relate and
check for understanding
1 hr. class
time for
nucleotides,
1 hr. class
time for
amino acids
Nucleotide changes: What types
of changes occur most often
(usually purine for purine or
pyrimidine for pyrimidine);
In which position of the codon
do most nucleotide changes
occur (3rd, then 1st, and rarely
2nd) – initiate class discussion
(students usually know and
apply wobble hypothesis); What
are the different classes of
amino acids (polar, nonpolar,
acidic, basic); How do amino
acids affect the structure and
function of a protein (polarpolar, nonpolar-nonpolar, and
acidic-basic interactions affect
protein folding/conformation
which determines function)
GATE: investigate
the different genetic
codes; compare and
contrast
EL: check for
understanding of
relevant vocabulary
GATE: using PDB,
identify regions of
COI in which
nucleotide changes
occur/don’t occur
Section 3: Science Literacy
Content Objective: Using nucleotide changes in specimen DNA barcodes (Channel Island
rockfish), apply parsimony and nearest neighbor analysis to create a phylogenetic tree for the
class species
Language Objective: Students will become fluent in the use of relevant biological terms related
to DNA barcoding and their research.
Lesson Plan Template
Assessment: How will I know students met the objective?
Students will prepare a scientific manuscript for publication which will be submitted to an
appropriate journal (National High School Journal of Science, Journal of Experimental
Secondary Science, Journal of Youths in Science, Torrey Pines Falconium Journal, etc.)
Rubric:
Assessment criteria
1. Students follow the format for the journal to which they submit their manuscript.
2. Students introduce the research topic and provide sufficient background information for
general understanding.
3. Students clearly state the questions and/or hypotheses being addressed in the research.
4. Students describe the experimental procedures utilized to address the questions/hypotheses.
5. Students present the data in appropriate tables.
6. Students use appropriate analytical and statistical methods to interpret data.
7. Students thoroughly discuss and explain research results, relating them to current scientific
theories and applications.
Description of lesson: Students will use the nucleotide differences identified in the specimen
DNA barcodes to construct a phylogenetic tree, and will analyze the evolutionary relationship of
the included species and instances of speciation in progress
Time required for the lesson:
Materials/ Preparation needed: DNA barcode sequences on BOLD-SDP (www.boldsystems.org)
Description of
Student Task (each
step)
Students use
tabulation of
nucleotide differences
to quantify
intraspecific and
interspecific
differences; students
create phylogenetic
trees (rooted and
unrooted) and
Time
Needed
for
Students
to
complete
each
Task
1 hr.
class
Teacher Notes
(Include strategies/questions
to check for understanding)
Accommodation/Modification
for Student Access and
Extension (i.e. strategies for
EL and extensions for GATE)
Allow students to begin to
grind through the analysis
(30 min) and then
demonstrate the power of
computational biology to
produce the phylogenetic
tree instantaneously; What
relationships do we see
EL: check for understanding
of relevant vocabulary
GATE: write computer
programming code to rank
number of nucleotide
differences between
specimens
Lesson Plan Template
phylograms using
bioinformatics
Analyze the
phylograms to
determine
evolutionary
relationships and
instances of
speciation in progress
1 hr.
class
Compare the number of
nucleotide differences
within a species to the
number between different
species (fewer differences
within a species <2%, more
differences between species
>2%); How can the process
of speciation be identified
(on a phylogram, specimens
within a species begin to
approach the 2%
difference); What processes
can lead to speciation
(geographic isolation,
reproductive isolation, etc.)
Section 4: Student Pages
Please provide a printer/copier friendly student pages for Section 2 and Section 3.