Text: Prepared by the Instructor
DESCRIPTION: Biotechnology Research Project explores the
science of genetic engineering through a class research project. With an experimental focus, students receive
the molecular background and the laboratory techniques, culminating in DNA
sequencing and analysis. They chose a
target organism(s), target gene(s), design primers, amplify their gene of
interest using PCR, and sequence the gene. They finally prepare and present a
poster with their findings to the scientific community and/or offer workshops
for the educational community.
Student
Objectives:
regarding the Limulus Grant
-use
a constructivist approach utilizing a target organism and genes
-work
in conjunction with the university partnerships, but independently of them
-employ
alternative assessments: structured controversies, position papers, concept and
Vee mapping
-integrate
bioinformatics as a tool to obtain and analyze data
-publish
and present class research results
Grading
and Assessment:
Data/graphing
notebook and folder are required. Lab
reports are completed in Vee Map format complete with
concept map and flow chart, typed. All handouts, completed assignments and
tests are organized in the folders.
Students present posters to the teaching and scientific communities as
well as mentor teachers/students from other schools during workshops held at
this school or neighboring schools.
Grading Policy: tests/concept maps: 40%; labs: 30%; homework/participation:20%
Make-up
Work: Students are expected to be prompt
and prepared for class. In the event of
missing homework, the student is expected to email the instructor if work is
not available on the website. Should a
student be absent on the day of a test, she is expected to make up that test ON
the day of her return, either during free time or after school. Make up work for an extended illness (more
than 2 class days, will be arranged with the teacher.)
Note:
because of the orientation and focus of this class, there are more lab
assignments than tests.
COURSE OUTLINE:
Introduction
to Biotechnology
Expectations
Procedural Plan
Background
Information: Molecular level
Structure and Function of Nucleic
Acids: Central Dogma revisited
Post Transcriptional and Post Translational
Modification
RNA folding, RNAi,
snRNA
Protein structure and function
Comparison of mtDNA to nDNA
Use of NCBI: Structure, Cn3d and OneDViewer
DNA
Extractions and Purification
DNA
Quantification by UV Spectrophotometry
Use
of Bioinformatics Tools for data and analysis
NCBI: PubMed,
OMIM, and Entrez
ClustalW
as an alignment tool
Primer3
Primer
Design and PCR Protocol
Use of NCBI: Taxonomy Browser
Primer math and template calculations
Use of Primer3 for primer analysis
Solution preparations
In
vitro DNA Synthesis: PCR of gene of interest
Analysis of
PCR Product by Agarose Gel Electrophoresis
Photodocumentation
Purification
of PCR Product
Quantitation of DNA Template: PCR Product
Automated
DNA Sequencing: ABI Prism 310 Genetic Analyzer
Primer
math and template calculations for sequencing
Cycle Sequencing Reactions
Purification of Extension Products
Resuspension, Sequencing and Conversion
of Raw Data
Data Analysis by NCBI: BLAST
Genotyping
Procedures and Applications
Use
of Gene Mapper