draft 2/2001
Biology Student WorkBench

A Bioinformatics Resource:

Molecular Investigations and Tutorials

Version 1.0 August 2000

See http://bioquest.org/bioinformatics for updates

An Education, Outreach and Training Partnership for Advanced Computational Infrastructure (EOT-PACI) Partnership

NCSA, UIUC College of Education, and BioQUEST Collaboration

Funded in part by NSF Award - #9950689

You are currently viewing an archived version of this material. 
For the current Biology Student Workbench Project please visit 
BioQUEST/bioinformatics or Biology Student Workbench
Here are a number of linked investigations and tutorials that are in the developmental phase by the Biology Student WorkBench project collaborators: 
Scott Cooper
University of Wisconsin La Crosse 

Scott leads project called BioWeb, a collaborative website produced by faculty members from 14 different University of Wisconsin System universities and centers.  By pooling our resources we hope to improve the quality of biology education at all of the UW-System institutions.

The materials presented here are part of a larger collection, which is available at the BioWeb site. The full collection has introductions to other topics in molecular genetics including gene sequencing, reverse complementation, protein motifs, and restriction mapping. 


Catabolite Activator Protein Homework
This is a homework assignment that involves studying the molecular mechanism by which Catabolite Activator Protein (CAP) [also called cAMP Receptor Protein (CRP)] binds to the promoter of the lac operon. It uses Chime to visualize the molecular interactions and asks students to consider the effects of a base substitution. 
Intron/Exon Splice Sites
This is a brief introduction to what intron/exon splice sites are and how they can be used to find genes. There is an exercise that involves using GENESCAN, BLASTP and UniGene to identify a putative gene and learn more about it.
Primer Design
This activity addresses some of the issues involved in designing primers (short unique base sequences that can be used to identify DNA regions, initiate PCR, etc.). It has a short introduction to primers and two exercises in primer design.
This short exercise has students align sequences using the Biology WorkBench and the analysis software from the National Center for Biotechnology Information.
This activity gives students a sense of what it is like to work with raw sequence data to build contigs (overlapping clones arranged to produce a contiguous region of a chromosome). It describes the role of artificial chromosomes, sequence tagged sites (STS), primers and PCR in doing genomic analysis. The activity has sequence data from four segments of human genomic DNA and asks students to identify STS's, build the contig and then look for an intron/exon splice sites within the sequence.
Generation of Phylogenetic Tree based upon DNA sequence analysis
A short exercise that has students build and interpret a phylogeny of some primates (including humans and Neanderthals) using mitochondrial D-loop sequences.
Ajit Chary

Kristian Engelsen

Nick Exner

Heather Grisco

Nerma Jahic

Meg Loven

Jamie L. Lynch

Deanna M. Raineri

Dr. Sandra Rodriguez-Zas

John M. Sabo

This collection of tutorials was developed by students and faculty at the University of Illinois-Champaign Urbana. Many of these materials were created under the supervision of Dr. Eric Jakobsson (jake@ncsa.uiuc.edu) as part of his work at the Computational Biology Group in the National Center for Supercomputing Applications.

Myoglobin as a Probe for Understanding Molecular Evolution
This Biology WorkBench tutorial uses the myoglobin gene to establish evolutionary relationships between various animal groups. After a brief introduction to the protein the tutorial explains how to find the sequence for human myoglobin. This sequences is then used as a BLAST probe to find myoglobin sequences from other organisms. By aligning sequences and using one of the tree building tools it is possible to estimate phylogenies based on this gene.
Study of Developmental Proteins in Drosophila
"You are one of the worlds leading scientists, and you have been doing genetic research with the species Drosophila Melanogaster (a.k.a. fruit flies). One day you stumble into the lab and notice that one of your specimens has a pair of legs growing out of its head! ..." 
This Biology WorkBench tutorial takes you through a study of antennapedia that includes searching databases, aligning/comparing sequences, and looking at molecular structures with the chime software. It also includes a short glossary and references to additional information. 
Studying Limb Dysplasia Using Bioinformatics
This Biology WorkBench tutorial is built around growth factor proteins (gdf5 and CDMP1) and how changes in their sequence/structure can cause abnormal limb development. After an brief introduction to the biology the tutorial helps you search, align/compare, and use the Rasmol software to look at the quatarnary structure of the proteins. A brief glossary and several references are also included.
Cystic Fibrosis Tutorial
"CF affects approximately 1 in 2000 people in United States and is the most common lethal genetic disease of Caucasians. ..." This Biology WorkBench tutorial explores the molecular basis for cystic fibrosis (the CFTR gene) by providing examples of how to search databases, align sequences, build phylogenetic trees, and predict transmembrane regions of protiens. I has extensive introductory material and several references for further information.
How to Use the Biology Workbench
This important resource provides an introduction to the features and tools available in the Biology WorkBench. These pages can be used as a way to orient to the Biology WorkBench or as a reference as questions arise. There are lists of the tools available in each section of the WorkBench and information on how to construct a query and import sequences. 
Sickle Cell Anemia Tutorial
"Sickle cell anemia is a disease in which the patient's red blood cells have an abnormal shape much like that of a sickle. These sickled red blood cells are very fragile and the result is severe anemia, or decreased number of red blood cells. ..." After a brief introduction to searching for and aligning sequences this Biology WorkBench tutorial focuses on using Rasmol to understand the point mutation to the beta-hemoglobin chain that causes sickle cell anemia. It includes copies of the structure files for normal and sickled proteins and lots of links to additional resources.
Paul Lock
Teacher, Urbana High School

Paul has used the Biology WorkBench in his courses for several years. He works closely with the group at University of Illinois.

Comparing Primate Proteins
"In this lesson, students should answer the two following questions: How are human proteins similar and different to other primates? Can the Differences show evolutionary trends? ..." The exercise starts with a pencil and paper acitivity that helps students develop and interpret a distance matrix by comparing amino acid sequences. Next students move to the Biology WorkBench and build phylogenetic trees based on hemoglobin sequences. 
Garry Duncan
Nebraska Wesleyan University 
The Biology WorkBench:  A Molecular Biology Discovery Tool for Studying Evolution
The following exercise will act as a springboard to empower students who wish to pose evolutionary questions that can be solved by analyzing molecular data. To accomplish this end, students must have a user-friendly interface that enables them to access DNA and protein databases, perform alignments and produce distance matrices and phylogenetic trees in order to answer their questions. The Biology Student Workbench (hereafter known simply as the workbench), developed by NCSA, provides this user-friendly interface.
Using PROTEIN EXPLORER to Visualize Mutation vs. Conservation in 3D from a Multiple Protein Sequence Alignment
Amino acid sequences retrieved from databases can be aligned using software such as the Biology Workbench (NCSA), and the alignments imported into Protein Explorer (PE) where mutations or conservation may be visualized in 3D. The following procedures allow you view in 3D an aligned protein sequence of enolase, an enzyme found in all living organisms because of its role in glycolysis.

Ethel Stanley
Keith Stanley
Beloit College 

Looking into Glycosidases: A Bioinformatics Resource for Biology Students

Editable Word Doc (2.3 MB)     PDF Version (1 MB)

Utilizing strategic molecular investigations, bioinformatics, and visualization tools in undergraduate biology is supported here by a number of scenarios for investigation.  Several introductory molecular problem spaces are featured with appendices on the glycosidases, resources, internet tools, and selected literature.  NOTE: None of these scenarios comes with a solution.  We generated many supportable hypotheses while working on the problems and hope you will enjoy similar success!

Information about CHIME

For more information on this project and useful links please see: 

You are currently viewing an archived version of this material. 
For the current Biology Student Workbench Project please visit 
BioQUEST/bioinformatics or Biology Student Workbench