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EXPLORING DNA STRUCTURE

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Bio21 materials

2006 Chautuaqua




Teaching materials

This page contains links to:new book

that have been developed over the past few years. Links to commonly-used web sites are included at the bottom of the page.

Use policy: Materials in this section of the site are freely available for educational use. We do ask, though, that instructors respect our copyright and reference www.geospiza.com when using these materials.

  Funding for this project was provided by the National Science Foundation's Course,   Curriculum, and Laboratory Improvement Program under grants DUE-0088153 and DUE-  0127599, also from Bio-Link, an NSF Advanced Technology Education Center.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation.
Data Sets Description

Nucleotide sequences

 BLAST for beginners

Mitochondrial sequences
Protein sequences Colonno, et. al HIV protease sequences after drug selection

Watkins, et. al. HIV protease sequences changing over time

HIV sequence key
3D structures Protein structures
Discrepancy results and contig sequences from Phrap assemblies
Gene sequence Clinical information (links to OMIM) Phrap Data
COMT Catechol-o-methyltransferase COMT-DQV plot
F13A1 Coagulation Factor VIII, A1 peptide F13A1-DQV plot
HBB Hemoglobin beta chain HBB-DQV plot
LIPC Hepatic Lipase LIPC-DQV plot
Supplements Using Entrez to find information

instructor version (590kb), student version ( 250kb)

Introduction to protein structure
Worksheets
Get Adobe ReaderPlease note, we have had reports of problems with Acrobat Reader version 6. if you have trouble with downloading or opening the worksheets, we recommend upgrading Acrobe Reader to version 7. Acrobat Reader is freely available from Adobe Systems Inc.
Allelic Variants of Superoxide Dismutase
 Find different kinds of information about a genetic disease and determine where the a mutated amino acid is located in the protein.

Activity ( 52kb)

Answers ( 72kb) * requires password to open
BLASTing through the kingdom of life Identify and find information about DNA sequences from all kingdoms of life.

Activity ( 272kb)

Answers ( 28kb) * requires password to open
Head, Shoulders, Knees, and Toes: Looking for Tissue-Specific Expression with BLAST

Learn why shoulders are shoulders and toes are toes. Students use this activity to explore when and where genes are expressed.

Activity ( 224kb)

Answers ( 148kb) * requires password to open
Mitochondria and Chloroplasts Mitochondrial sequences are often used in forensics as a tool for identification. Can you identify the source of a mitochondrial sequence? This worksheet provides points to consider in this type of analysis.

Investigating Maternal Inheritance
Tutorials
BLAST for beginners A painless introduction for those who have never used BLAST. A set of test sequences is supplied at the end.
Allelic variants of Superoxide Dismutase
  • Read about people with a genetic disease
  • Locate background information about a genetic disease
  • Find a gene map in the Entrez Gene database, look at the chromosomal location, exons, gene, transcript, and protein
  • Use OMIM to obtain a list of mutations (allelic variants) in a gene and look at the phenotypes
  • Find where a mutation is located within the three dimensional structure of a protein using Cn3D
  • Locate full-text papers in PubMed (a database of scientific literature)
Cancer Biology
  • Use Entrez to efficiently locate scientific articles in PubMed
  • Learn about MeSH (Medical Subject Headings)
  • Learn how to use Boolean operators (AND, OR, NOT), the wildcard operator (*), and how to combine search terms
Introduction to Protein Structure
  • Learn how to use Cn3D - an application for viewing and comparing protein structures
  • Learn how to find structures in the molecular modeling database (MMDB)
  • Learn about the different levels of protein structure
  • Learn about the relationship between the structure and function of a protein
  • Learn about the relationship between the amino acid sequence and physical properties of a protein (charge, hydrophobicity, element, etc.)
Mitochondria and Chloroplasts
  • Use bioinformatics tools to study mitochondria and chloroplasts
  • Study maternal inheritance
  • Compare human mitochondria with mitochondria from other animals
  • Learn about human evolution
SNP or Sequencing Error?
  • Use information from phred to evaluate sequence quality
  • Use information about phrap assemblies to evaluate assemblies and to find potential polymorphisms
  • Use the CGAP SNP index as a tool for evaluating potential SNPs
  • Use dbSNP and BLAST to evaluate potential SNPs
Graphing Scientific Data with Microsoft Excel Part I. Prepare a straight line plot using Microsoft Excel and get the correct values on the both the X and Y axis.

Part II. Prepare and edit a semi-log plot with the log scale on the Y axis.
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