This is a list of helpful Bioinformatics web sites, including those with interactive tutorials.
The EBI (European Bioinformatics Institute) provides a number of 2Can tutorials for their bioinformatics tools. This is as good way to find out about which nucleotide and protein analyses are available and how they work. In these EBI tutorials you will be guided through a series of exercises using sample fragments of sequence. To gain more information about these sequences, you will use a variety of tools that are available at the EBI to compare the sequences to databases and analyse them.
The NCBI (America's National Center for Biotechnological Information) also provide very useful set of interactive bioinformatics tutorials, together with listings and definitions of various tools. Although there are fewer individual guides than at the EBI, those that are given give more explanation and are an excellent place to learn about BLAST and PSI_BLAST.
Also at the NCBI it is worth considering the Coffee Break archive, that provides a series of reports which are usually based on a real biomedical discovery reported in the published peer-reviewed literature. The result is an interactive tutorial using NCBI tools that tells a biological story. The archive has not been updated recently but is still invaluable in illustrating how things are done using the various tools and resources. At various points in each report the reader can see the evidence and find further related information using predefined searches; like PubMed searches of MEDLINE, and BLAST searches of GenBank.
There are many bioinformatics tools and services available from Cambridge at the School of Biological sciences bioinformatics website. Of special note are the run locally at the university, which range from the use of individual programs and services to learning how to write computer programs for biology.
If you need to draw up the structures of a protein or any homologues whose structures have been solved, a good place to start is at the Protein Data Bank website. There is an online tutorial and various training materials on how to use the PDB. Also of interest are narrated screencasts that illustrate the RCSB PDB website,
Finally, for the Part II Biochemistry PBL exercise and associated teaching there will be a significant focus on web sites where you can perform multiple analyses across multiple databases without having to go to multiple web sites. The most important of these are the Ensembl Genome browser and the EBI Services.