Annotated Links to Educational Web Materials
for Molecular Biology and Bioinformatics
Dr. Donna E. Crone, Research Associate and Lab Manager
Dept of Biology, Rensselaer Polytechnic Institute
Restriction Analysis Exercise
Amino Acid Animation
DNA from the Beginning: http://www.dnaftb.org/dnaftb/ each concept includes animation of experimental procedure to illustrate concept, accompanying interactive problem set. Also available on CD set for purchase.
Molecules of Genetics
Concept 22: DNA words are three letters long.(genetic code, translation)
Concept 23: A gene is a discrete sequence of DNA nucleotides. (DNA sequencing)
Concept 24: The RNA message is sometimes edited. (2 sections: a)restriction enzymes, agarose gel electrophoresis, b)introns and exons) -- excellent problem set for restriction mapping
Genetic Organization and Control
Concept 33: Genes can be turned on and off. (lac operon, control of gene expression)
Concept 34: Genes can be moved between species. (recombinant DNA transformation, insulin production in bacteria) -- problem set recombinant GFP
Concept 36: Different genes are active in different kinds of cells. (gene expression, gene chip and DNA array technology)
Concept 39: A genome is an entire set of genes. (Human Genome Project: ESTs, BACs, mab based approach, shotgun approach)
Biology Animation Library: http://www.dnalc.org/resources/BiologyAnimationLibrary.htm
Polymerase chain reaction, southern blotting, cycle sequencing
Biointeractive Virtual Labs: http://www.biointeractive.org/
Bacterial Identification Lab is excellent.† Interactive "lab" section with accompanying notebook for reference and explanation.† Sample prep (select virtual colony isolate DNA ), PCR amplification, PCR purification, sequencing prep, DNA sequencing and sequence analysis (BLAST of obtained sequence to determine identity of isolated colony).
May request CD of educational materials free from HHMI with registration.
Kimballís Biology Pages: http://www.ultranet.com/~jkimball/BiologyPages/
Supplement to concepts presented in class.
NCBI Bookshelf - http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Books
Includes Molecular Biology of the Cell (3rd ed 1994) and Molecular Cell Biology (4th ed. 1999).
Animations from Molecular Cell Biology are linked to figures.
A particular favorite is :Chromosome Packing Figure 9-35 http://www.ncbi.nlm.nih.gov:80/books/bv.fcgi?call=bv.View..ShowSection&rid=mcb.figgrp.d1e34827 with link to quicktime movie of three dimensional packing of nuclear chromosomes.
UCLA Molecular Biology Tutorials
http://www.lsic.ucla.edu/ls3/tutorials/gene_cloning.html Restriction enzymes, sequencing, southern, PCR
http://www.lsic.ucla.edu/ls3/tutorials/gene_expression.html Transcription, splicing, translation. I use the splicing tutorial in class to illustrate the steps in splicing.
Introduction to Protein Structures
Protein Structure - supplementary links to understand protein structure
overview of amino acids from Kimball's biology pages
animation of amino acids and formation of higher levels of structure from John Kyrk
includes structures of each of the amino acids as well as animation of alpha helix and beta sheet
Amino Acids and Protein structure - Recombinant DNA course CSUN- Stan Metzenberg
Hydrogen bonds - Kimball's Biology pages
Chemical Bonds and Important Biological Molecules including vander Waals forces, electrostatic interactions and hydrophobic effects
Molecules of Life http://biop.ox.ac.uk/www/mol_of_life/Molecules_of_Life.html
Particularly relevant to the Bioinformatics workshop are the sections on proteins and protein structure prediction.
This site includes a "roller coaster" exploration of protein structure: http://biop.ox.ac.uk/www/mol_of_life/roller.mpg.
Molecular Biology Tools: Restriction Analysis Programs
Webcutter : http://www.firstmarket.com/cutter/cut2.html
Enter sequence, choose linear vs circular, select restriction sites, returns sequence with marked sites and list of sites not present in sequence, table of sites
Donna E. Crone ©2002 for Bioinformatics Workshop last modified May 9, 2004
Enter sequence, choose linear vs circular, submit
Program cuts DNA with all enzymes in
database returns graphical map NEB
May view list of fragments and/or virtual gel of fragments
Option for custom digests using one or more enzymes with sites in sequence