PPS '96 Syllabus

Course Index Syllabus Index Term 2

Term 1

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Section 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

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  Section 2

• 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

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  Section 3

• 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

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  Section 4

• / 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

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  Section 5

• 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
    • EMBL database
    • GenBank
  • 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

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  Section 6

• 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