PPS '97Syllabus
Course Index
Syllabus Index
Term 2
Term 1
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Introduction: outline of proteins-
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what are they?
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what do they do?
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why is it important to study them?
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Introduction to The Internet
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The network
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Telnet
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e-mail
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newsgroups
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FTP
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Gopher
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WWW; Hypertext, HTML, Browsers and their configuration
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MOOs; BioMOO
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Primary Structure:
the 20 amino acids - chemical structure & properties:
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chirality
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different types of side chain: relevance to mutation
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size
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aliphatic/aromatic
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polarity
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charge
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hydrophobicity;
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disulphide bonds
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molecular models
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Introduction to RasMol
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Software archives
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Polypeptide geometry:
the folding chain
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nomenclature
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peptide bond
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torsion angles:
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main chain phi/psi - helices, sheets, turns;
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side chain rotamers
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Ramachandran plots
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molecular surfaces; molecular graphics
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MAGE, PREKIN
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Introduction to Bioinformatics:
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sequence » structure
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evolution and mutation
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genetic information- the triplet code; DNA structure
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/
Synthesis of proteins:
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cell biology background;
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transcription:
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mRNA
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RNA polymerase
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introns, exons, splicing
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translation:
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ribosomes
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tRNA
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start/stop codons
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Post-translational processing:
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ER-directed vs. cytoplasmic
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signal peptides
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peptidase
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foldases
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glycosylation
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myristoylation
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oligomerisation
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binding of co-factors, etc
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Transport:
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into ER
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to Golgi
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lysosomes & export
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to and across membrane, etc
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Degradation
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Biological Information
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Networks
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WWW, CERN
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EMBnet; EMBL Database, SEQNET, HGMP-RC
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European Bioinformatics
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ExPASy
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EMBL; Hamburg, Grenoble, EBI outstations
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USA Bioinformatics
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NCBI, GenBank, NLM, NIH, BNL
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Sequence Databases and
Sequence Analysis:
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genomic, cDNA
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protein sequence
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OWL; SWISS-PROT , PIR, GenBank (translation),NRL-3D, PDB
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Similarity searching: BLAST, FASTA
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Searching secondary sources: motifs, patterns, rules, profiles
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PROSITE, ProfileScan, BLOCKS, PRINTS, ALIGN
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Genome databases: GDB, MGD, FlyBase, Saccharomyces etc
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Experimental considerations:
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How are genes actually sequenced; PCR
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Production of cDNA
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Web authoring, with bioinformatics
and protein structure in mind
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Writing HTML
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Search and other forms: scripts
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Graphics:
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using RasMol and other molecular graphics software
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painting drawing and other packages
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imagemaps
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MPEGS and other movie formats
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copyright , Birkbeck College,1995-1997 all rights reserved worldwide