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.
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.
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.
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.
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 (firstname.lastname@example.org)
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
|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
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.
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
"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
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.
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.
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.
"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.
Nebraska Wesleyan University
Biology WorkBench: A Molecular Biology Discovery Tool for Studying
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
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.
into Glycosidases: A Bioinformatics Resource for Biology Students
Editable Word Doc (2.3
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!