PPS '97Syllabus

Course Index

Syllabus Index Term 2

Term 1

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
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
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
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
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
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

PPS '97Syllabus

Term 1

Section 1

Section 2

Section 3

Section 4

Section 5

Section 6