Lecture 3, 04/09/16, tue In this lecture, we covered some more details of the basic processes of gene expression (transcription, RNA maturation, translation), discussed the structure and organisation of genomes as well as fundamental controll mechanism for gene expression and protein activity, and gave a brief overview of some basic issues in reproduction, evolution, and phylogeny. We also discussed some exceptions to the universal genetic code that involve mechanisms based on RNA secondary structure. Important concepts include: - RNA maturation, splicing, introns, exons - eukariotic genome structure, chromosomes, extranuclear genomes (mitochondrial, chloroplast) - function of genomic dna: protein coding, functional rna coding, centromeres, telomeres, repetitive elements, transposons, ... - gene regulation: transcription / translation control, transport control, RNA maturation control, mRNA degradation control, protein activity control; regulatory networks - evolution: dna replication, mutations (transitions / transversions, insertions, deletions, transposons, chromosome recombination, cross-over) Note: - genome size / chrosome number is not strictly correlated to complexity of organism - gene regulatory relationships can have the form of (noisy) logical conjunctions or disjunctions (AND/OR expressions) and can be modelled using standard CS concepts (gates, neural networks, ...) - mutation probabilities vary across chromosomes (hot spots) - mutations result in genomic differences that can be used to estimate evolutionary relationships / distance between organisms Resources: - Garret and Grisham: Biochemistry. Saunders College Publishing, 1995 (Parts of Chapters 1-7) - Alberts, Bray, Lewis, Raff, Roberts, Watson: Molecular Biology of the Cell. Garland Publishing, Inc., 1994 (Parts of Chapters 1-7) - Benjamin Lewin: Genes V. Oxford University Press, 1994. - Griffiths, Miller, Suzuki, Lewontin, Gelbart: An Introduction to Genetic Analysis. Freeman and Company, 1993. - Watson, Gilman, Witkowsi, Zoller: Recombinant DNA. Scientific American Books, 1992. Assigned Reading (reminder): - Douglas R. Hofstadter: Metamagical Themas, Chapter 27: The Genetic Code: Arbitrary? Bantam Books, 1986 [Available from the CPSC 445/545 box in the ICICS Reading Room]