20.1 Introduction 20.2 Eukaryotic RNA polymerases consist of many subunits 20.3 Promoter elements are defined by mutations and footprinting 20.4 RNA polymerase I has a bipartite promoter 20.5 RNA polymerase III uses both downstream and upstream promoters 20.6 The startpoint for RNA polymerase II 20.7 TBP is a universal factor 20.8 TBP binds DNA in an unusual way

22.1 Introduction 22.2 Nuclear splice junctions are short sequences 22.3 Splice junctions are read in pairs 22.4 Nuclear splicing proceeds through a lariat 22.5 snRNAs are required for splicing 22.6 U1 snRNP initiates splicing 22.7 The E complex can be formed in alternative ways 22.8 5 snRNPs form the spliceosome

9.1 Introduction 9.2 Transcription is catalyzed by RNA polymerase 9.3 The transcription reaction has three stages 9.4 A stalled RNA polymerase can restart 9.5 RNA polymerase consists of multiple subunits 9.6 RNA Polymerase consists of the core enzyme and sigma factor 9.7 Sigma factor is released at initiation 9.8 Sigma factor controls binding to DNA 9.9 Promoter recognition depends on consensus sequences

11.1 Introduction 11.2 Lytic development is divided into two periods 11.3 Lytic development is controlled by a cascade 11.4 Functional clustering in phages T7 and T4 11.5 Lambda immediate early and delayed genes are needed for both lysogeny and the lytic cycle

16.1 Introduction 16.2 The retrovirus life cycle involves transposition-like events 16.3 Retroviral genes codes for polyproteins 16.4 Viral DNA is generated by reverse transcription 16.5 Viral DNA integrates into the chromosome 16.6 Retroviruses may transduce cellular sequences 16.7 Yeast Ty elements resemble retroviruses 16.8 Many transposable elements reside in D. melanogaster 16.9 Retroposons fall into two classes 16.10 The Alu family has many widely dispersed members

14.1 Introduction 14.2 Breakage and reunion involves heteroduplex DNA 14.3 Double-strand breaks initiate recombination 14.4 Double-strand breaks initiate snapsis 14.5 Bacterial recombination involves single-strand assimilation 14.6 Gene conversion accounts for interallelic recombination 14.7 Topological manipulation of DNA 14.8 Specialized recombination involves breakage and reunion at specific sites 14.9 Repair systems correct damage to DNA 14.10 Excision repair systems in E. coli 14.11 Controlling the direction of mismatch repair 14.12 Retrieval systems in E. coli 14.13 RecA triggers the SOS system 14.14 Eukaryotic repair systems

25.1 Introduction 25.2 Oligosaccharides are added to proteins in the ER and Golgi 25.3 The Golgi stacks are polarized 25.4 Coated vesicles transport both exported and imported proteins 25.5 Different types of coated vesicles exist in each pathway 25.6 Cisternal progression occurs more slowly than vesicle movement 25.7 Vesicles can bud and fuse with membranes 25.8 SNAREs control targeting 25.9 The synapse is a model system for exocytosis 25.10 Protein localization depends on specific signals 25.11 ER proteins are retrieved from the Golgi 25.12 Brefeldin A reveals retrograde transport 25.13 Receptors recycle via endocytosis 25.14 Internalization signals are short and contain tyrosine

28.1 Introduction 28.2 Transforming viruses carry oncogenes 28.3 Early genes of DNA transforming viruses have multifunction oncogenes 28.4 Retroviruses activate or incorporate cellular genes 28.5 Retroviral oncogenes have cellular counterparts 28.6 Ras oncogenes can be detected in a transfection assay 28.7 Ras proto-oncogenes can be activated by mutation at specific positions 28.8 Nondefective retroviruses activate proto-oncogenes 28.9 Proto-oncogenes can be activated by translocation 28.10 The Philadelphia translocation generates a new oncogene 28.11 Oncogenes code for components of signal transduction cascades 28.12 Growth factor receptor kinases can be mutated to oncogenes 28.13 Src is the prototype for the proto-oncogenic cytoplasmic tyrosine kinases 28.14 Oncoproteins may regulate gene expression 28.15 RB is a tumor suppressor that controls the cell cycle 28.16 Tumor suppressor p53 suppresses growth or triggers apoptosis

2.1 Introduction We can think about mapping genes and genomes at several levels of resolution: A genetic (or linkage) map identifies the distance between mutations in terms of recombination frequencies. A linkage map can also be constructed by measuring recombination between sites in genomic DNA

7.1 Introduction 7.2 Codon-anticodon recognition involves wobbling 7.3 tRNA contains modified bases that influence its pairing properties 7.4 (There are sporadic alterations of the universal code) 7.5 tRNAs are charged with amino acids by synthetases 7.6 Accuracy depends on proofreading 7.7 Suppressor tRNAs have mutated anticodons that read new codons 7.8 The accuracy of translation 7.9 tRNA may influence the reading frame