A Computer Scientist’s Guide to Cell Biology

Table of Contents
List of Figures ........................................................................... xi
Introduction............................................................................. xiii
How Cells Work ......................................................................... 1
Prokaryotes: the simplest living things ..................................................1
Even simpler “living” things: viruses and plasmids ..............................4
All complex living things are eukaryotes...............................................6
Cells cooperate .......................................................................................9
Cells divide and multiply .....................................................................14
The Complexity of Living Things........................................... 19
Complexes and pathways .....................................................................19
Individual interactions can be complicated..........................................21
Energy and pathways............................................................................29
Amplification and pathways.................................................................31
Modularity and locality in biology.......................................................33
Looking at Very Small Things................................................ 37
Limitations of optical microscopes ......................................................37
Special types of microscopes ...............................................................39
Electron microscopes............................................................................42
Manipulation of the Very Small ............................................. 45
Taking small things apart. ....................................................................45
Parallelism, automation, and re-use in biology....................................53
Classifying small things by taking them apart .....................................55
Reprogramming Cells ............................................................. 59
Our colleagues, the microorganisms ....................................................59
Restriction enzymes and restriction-methylase systems......................59
Constructing recombinant DNA with REs and DNA ligase................60
Inserting foreign DNA into a cell.........................................................62
Genomic DNA libraries........................................................................64
Creating novel proteins: tagging and phage display ............................65
Yeast two-hybrid assays using fusion proteins ....................................67
Other Ways to Use Biology for Biological Experiments ...... 71
Replicating DNA in a test tube.............................................................71
Sequencing DNA by partial replication and sorting ............................75
Other in vitro systems: translation and reverse transcription...............76
Exploiting the natural defenses of a cell: Antibodies...........................77
Exploiting the natural defenses of a cell: RNA interference ...............78
Serial analysis of gene expression........................................................79
Bioinformatics .......................................................................... 83
Where to go from here? .......................................................... 91
Acknowledgements ..............................................................................94
Index.......................................................................................... 95

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