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
http://www.rpi.edu/~croned/

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

Amino Acids

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

NEBcutter: http://tools.neb.com/NEBcutter/index.php3

Enter sequence, choose linear vs circular, submit

Program cuts DNA with all enzymes in NEB database returns graphical map

May view list of fragments and/or virtual gel of fragments

Option for custom digests using one or more enzymes with sites in sequence

Donna E. Crone ©2002    for Bioinformatics Workshop last modified May 9, 2004