PPS '96 Syllabus
Course Index
Syllabus Index
Term 2
Term 1
- Introduction: outline of proteins-
- what are they?
- what do they do?
- why is it important to study them?
- Introduction to The Internet
- The network
- Telnet
- e-mail
- newsgroups
- FTP
- Gopher
- WWW; Hypertext, HTML, Browsers and their configuration
- MOOs; BioMOO
- Primary Structure: the 20 amino acids - chemical structure & properties:
- chirality
- different types of side chain: relevance to mutation
- size
- aliphatic/aromatic
- polarity
- charge
- hydrophobicity;
- disulphide bonds
- molecular models
-
- Introduction to RasMol
- Software archives
- Polypeptide geometry: the folding chain
- nomenclature
- peptide bond
- torsion angles:
- main chain phi/psi - helices, sheets, turns;
- side chain rotamers
- Ramachandran plots
- molecular surfaces; molecular graphics
- MAGE, PREKIN
- Introduction to Bioinformatics:
- sequence » structure
- evolution and mutation
- genetic information- the triplet code; DNA structure
- / Synthesis of proteins:
- cell biology background;
- transcription:
- mRNA
- RNA polymerase
- introns, exons, splicing
- translation:
- ribosomes
- tRNA
- start/stop codons
- Post-translational processing:
- ER-directed vs. cytoplasmic
- signal peptides
- peptidase
- foldases
- glycosylation
- myristoylation
- oligomerisation
- binding of co-factors, etc
- Transport:
- into ER
- to Golgi
- lysosomes & export
- to and across membrane, etc
- Degradation
- Biological Information
- Networks
- WWW, CERN
- EMBnet; EMBL Database, SEQNET, HGMP-RC
- European Bioinformatics
- ExPASy
- EMBL; Hamburg, Grenoble, EBI outstations
- USA Bioinformatics
- NCBI, GenBank, NLM, NIH, BNL
- Sequence Databases and Sequence Analysis:
- genomic, cDNA
- protein sequence
- OWL; SWISS-PROT , PIR, GenBank (translation),NRL-3D, PDB
- Similarity searching: BLAST, FASTA
- Searching secondary sources: motifs, patterns, rules, profiles
- PROSITE, ProfileScan, BLOCKS, PRINTS, ALIGN
- Genome databases: GDB, MGD, FlyBase, Saccharomyces etc
- Experimental considerations:
- How are genes actually sequenced; PCR
- Production of cDNA
- Web authoring,
with bioinformatics and protein structure in mind
- Writing HTML
- Search and other forms: scripts
- Graphics:
- using RasMol and other molecular graphics software
- painting drawing and other packages
- imagemaps
- MPEGS and other movie formats
Course Index
Syllabus Index
Term 2
Last updated 11th Jun '96