Team:UCSF/Lincoln High School Curriculum

From 2008.igem.org

Latest revision as of 02:22, 29 October 2008

Lab Work @ George Class

1. Making Cheese and Yogurt – Traditional applications

2. Breeding Fruit Flies – The laws of inheritance

3. Micropipetting – Review of the metric system

4. Microbiology - Culturing Bacteria

- Identification of plasmid containing E. Coli

5. Isolation of Genomic DNA

- Cheek cell, kiwi, and bacterial DNA extraction

- Agarose gel electrophoresis#1: genomic DNA

6. Transformation I: pAMP – Griffith’s Experiment

7. Cutting Lambda - restriction endonucleases

- Digestion of Lambda and PhiX174 genomes

- Activity of ligase: ligate lambda Hind III fragments

- Agarose gel #2: viral genomes as molecular rulers

8. PCR I: Amplifying lambda – in vitro DNA replication

- Agarose gel #3: PCR reactions

9. Protein Purification

- pGlo Transformation and mini-fermentation

- GFP Purification – HIC hydrophobic chromatography

10. Protein Purification II – Bad Hair Day

- Ion exchange column chromatography

- Size exclusion chromatography

11. PAGE: Polyacrylamide gel electrophore of proteins

12. PCR II – DNA Fingerprinting

- Mapping Alu and DS180 polymorphisms

- Agarose gel #4: PCR products

13. ELISA Assay – antibodies and protein identification

- Introduction to assay development

14. Bioinformatics: Mitochondrial DNA Sequencing

- Genetic analysis using online DNA databases: the NCBI website

A Few Second-Year Lab Projects

1. Plating Libraries - Titering Phages

a. “Life cycle” of bacteriophage lambda GT10

2. Southern Blotting - Identification of specific DNA sequences

3. Western Blotting

a. Electro-transfer of protein

b. Ab conjugated probes with HRP marker

4. PCR Labs: GMO’s in our food

5. Recombinant DNA -Cloning using restriction enzymes and Ligase

6. PCR Cloning: Primer Design

CURRICULUM

The Genetics and Physiology of Cystic Fibrosis

Mendelian inheritance, genetics and probability, vocabulary, pedigree analysis, symptoms and therapies, social issues.

4 weeks LAB – 1, 2

The History of DNA Science

The experiments of: Darwin, Mendel, Sutton, Morgan, Beadle and Tatum, Griffith, Avery, Hershey and Chase, and Watson and Crick. An understanding of the scientific method and how we got to today’s technology are emphasized in this section.

4 weeks LAB – 3, 4, 5

The Biochemistry of DNA and Proteins

DNA biochemistry: replication, transcription, and translation. The genetic code, protein biochemistry, secondary and tertiary structure of proteins, the relationship between protein structure and function.

6 weeks LAB - 6,7,8

Gene Structure and Regulation

Upstream regulation: promoters, enhancers, transcription factors, signal sequences and transactivation. Downstream regulation: termination and polyadenylation. Genes: introns and exons, RNA splicing, coding region motifs, mutations, mutagenesis, consequences of mutation. 3 weeks

Molecular Biology: Applications, Implications, and Limitations

Genomic and plasmid DNA extraction and purification, restriction enzyme digestion, agarose gel electrophoresis, DNA ligation, transformation of E coli, selection for recombinant DNA, plating a phage library, PCR analysis of cheek cell scrapes, size exclusion, ion exchange, and HIC chromatography, polyacrylamide gel electrophoresis, and ELISA assays.

LAB - 10

Other methods

Fermentation and cell culture, in vitro mutagenesis, medically useful recombinant proteins, clinical trials, gene therapy, gene knockout, transgenic animals. Applications of biotechnology to medicine, agriculture, and the environment. Future directions and potentials.

Informatics

The genetic basis of identity testing, polymorphisms, RFLP’s and VNTR’s, DNA Sequence analysis, BLAST searches of NIH databases (EMBL/Swiss-prot), DNA editing software, hydrophobicity plotting, CHIME and Ras-Mol: protein modeling software.

5-6 weeks LAB - 11

The Genetics of the Immune System

A molecular analysis of the impact of molecular biology on immunology. Hematopoeisis, stem cell and myeloid cell differentiation, structure, function, and interactions of T cell and B cell subtypes, structure and function of five classes of antibody, antigen properties, the immune response, vaccines, genetics of the immune system. 3-4 Weeks LAB - 12, 13

Genethics

The Human Genome Project: ethical, legal, and social issues engendered by technology. Several scenarios are explored by students in preparation for a debate.

3 weeks

Cancer and AIDS: Biotech Has an Impact 2-3 Weeks

History of the epidemic, isolation of the virus, viral structure, viral replication, viral genetics, transactivating factors, effects on the immune system, host reactions, clinical course of the disease, therapies developed by the biotech industry. Cancer: carcinogenesis, genetics, clinical symptoms, angiogenesis, VEGF and inhibition by Avastin® in the treatment of colon cancer.

Principles of Biotechnology

Unit 1: Introduction to Biotechnology Industry: What Is Biotechnology? Three faces of Biotechnology: Research, Applied Science, Industry The Industry Pyramid: From Basic Research to Product Sales Ancient Biotechnology vs. Modern Biotechnology The Molecules of Biotechnology

Unit 2: Establishing a Context for the Study of Biotechnology: Genetic Diseases as Models for the Mechanisms of Human Inheritance Lorenzo’s Oil: ALD as a Model for the Mechanism of Sex-Linked Inheritance, Scientific Method In Action Understanding Cystic Fibrosis: A Model for the Mechanisms of Human Inheritance Good Genes Gone Bad: Overview of Human Genetic Diseases - 12 Genes How Good Genes Go Bad - in vivo mutagenesis The CFTR Gene and Its Protein Product How Biotechnology Impacts CF Treatments Testing for Genetic Disorders: Parental, PGD, Prenatal Testing Constructing and Interpreting Human Pedigrees Sex Determination: The SRY Gene

Unit 3: Digging Deeper: Factors That Complicate Inheritance, Beyond simple Dominant/Recessive Polygenic Inheritance Incomplete Dominance Multiple Allele Traits Environmental Effects Epigenetics: Ghosts in your Genes

Unit 4: History of DNA Science A Continuum of Discovery – Manipulation of DNA from Ancient Times to Now Focus on Organisms and Mechanisms of Inheritance: Darwin and Mendel Focus on Cells: Hooke to Morgan Focus on Molecules: Protein or DNA? Debunking Dogma

Unit 5: DNA Chemistry: How Can A Simple, Repetitive Molecule Be The Genetic Code? How Does It Work? Clues from the Chemists – Chemical Monomers and Base Pairing Clues from X-Ray Diffraction: Rosalind Franklin and photograph 51 Watson and Crick’s Model: Stability and Directionality

Unit 6: Restriction Endonucleases: Molecular “Scissors” Using the New England BioLabs Catalogue The Function of Restriction Endonucleases (vs. Exonucleases) Sources, Varieties of Endonucleases Conditions for Restriction Digests Restriction Maps Electrophoresis

Unit 7: DNA Replication Cell Life Cycle – The Timing of Replication. Mechanism of Replication: 7 Proteins Required for Replication In Vivo. Mechanism of Replication: Denaturing To Elongation Errors in Replication – Mutations In Vitro Replication – An Application of Biotechnology That Has Many Uses The Technique of the Decade: PCR –Compensating for In Vivo Proteins

Unit 8: Gene Expression - DNA Transcription DNA vs. RNA: Structural and Functional Differences Gene Structure Gene Regulation Stages of Transcription Transcriptional Regulation at the Upstream Regulatory Region Transcriptional Regulation in Prokaryotes Transcriptional Regulation in Eukaryotes Post-Transcriptional Modifications Prokaryotic vs. Eukaryotic Gene Expression

Unit 9: Gene Expression – Translation The Language of Genes: Using Codon Tables Steps in Gene Expression Requirements for Translation Ribosomal Structure/tRNA Structure/Mature mRNA Structure

Unit 10: Protein Structure, Function, and Purification Relationship of Protein Structure to Function Properties of Amino Acids Peptide Bonds/Polypeptide Chains Protein Structure: Polypeptide Folding Protein Purification – Methods

Unit 11: Genethics: The Implications of the Applications Introduction to Bioethics Relevant Scenarios: Current Issues in Bioethics GATTACA: Fantasy or Reality?

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