1. This Week Chapters 9, 10.1 and 10.4 - 10.7 for reference, –exam material will be on lecture content for the above, Chapter 11.5 (Friday). Monday Paper,

2. Seminars extra credit May 21 “Virgin Birth, Centrosomes, and Microbes”. William Sullivan, Molecular, Cell, & Developmental Biology, University of California, Santa Cruz May 28 "Proliferation & Caste Formation in a Polyembryonic Parasitoid Wasp". Laura Corley, Department of Entomology, Washington State University Wednesdays, 4:00 PM, BI 212

3. Gene Expression …the processes by which information contained in genes and genomes is decoded by cells,...in order to produce molecules that determine the phenotypes observed in organisms, –transcription (post-transcriptional modifications), –translation (post-translational modifications).

4. Transcription

5. ...the synthesis of mRNA from a DNA template, - now it is important to understand when and where, as well as how.

6. mRNA Synthesis Template (DNA) and Promoter, Nucleoside triphosphates (NTPs), –N: A,U,G,or C, Enzymes (RNA polymerases), Energy (as in replication, from phosphate bonds).

7. E. coli RNA Polymerase

8. RNA Transcription prokaryote

9. E. coli Promoter Sequences concensus sequence alignment

10. Promoter Regions Core Promoter ( ~ 0 to ~ -40 bp)Proximal ( ~ 100 - 200)

11. Regulation of Transcription (Prokaryotes) Regulation of gene expression is often at the transcription level, –Negative regulation, inducible, repressible, –Positive regulation Gene native state is “on”. Gene native state is “off”.

12. Negative Regulation (Inducible) …default state is “on”, i.e., the gene is transcribed. Protein! Protein, or metabolite, etc.

13. Negative Regulation (Repressible) …default state is “on”, i.e., the gene is transcribed. Protein! Protein, or metabolite, etc.

14. Positive Regulation …default state is “off”, i.e., the gene is not transcribed.

15. Eukaryotic Initiation Transcription is regulated by activators, repressors, co-activators and basal transcription factors.

16. Promoter Bashing Modulators of expression can act at great distances.

17. Drosophila Guts and Such dpp locus...(c)LE and (d) ID enhancer driven, give rise to fly appenages.

18. Terms cis-acting elements; –DNA sequences that serve as attachments sites for the DNA- binding proteins that regulate the initiation of transcription. trans-acting elements; –the DNA-binding proteins that regulate the initiation of transcription.

19. Chromatin Remodeling Expressed Proteins

20. Post-Transcriptional Events RNA processing, –splicing, –poly adenylation, Alternate RNA processing.

21. RNA can be Autocatalytic Group I and Group II introns, –found in mitochondria, chloroplasts, and sometimes in bacteria,

22. Group II Introns

23. Eukaryotic Intron Excision (not autocatalytic)

24. Eukaryotic Intron Excision (sequence is important)

25. Spliceosomes... small nuclear RNAs (snRNAs): –RNA molecules that act as catalysts in spliceosomes, catalytic RNAs that have probably evolved from ancient RNA enzymes (ribozymes). …work in concert with > 100 proteins to facilitate intron identification and removal, –snRNPs: RNA/Protein structures.

26. U1 and U2 U1 binds to the 5 ’ exon/intron junction. U2 binds to the adenosine at the branch site. Psuedouradine (  Think about the required specificity for intron identification in cells.

28. mRNA Processing splicing

29. Polyadenylation AAUAA: concensus poly-A recognition site. …complicated biochemistry, lots of sub-units.

30. Alternate mRNA Processing …recognition of different poly-A sites.…alternate splicing.

31. Complexity Calcitonin gene.

32. Central Dogma DNA RNA Protein transcription replication translation ? (alternately processed)

33. Genome... the dynamic complement of genetic material in an individual, Transcriptome... mRNA component in an individual, –complexity increases resulting from transcription control and transcription and post-transcription modification, Proteome... the protein component of an individual, –complexity increases due to post-translational modification, protein-protein interactions, etc. Expanded Central Dogma GenomeTranscriptomeProteome

34. Translation …the synthesis of a polypeptide. This occurs on ribosomes using the information encoded on mRNA, –tRNA molecules mediate the transfer of information between mRNA and the growing polypeptide.

35. Initiation complexity 1. Recent reports of “alternate” translation start sites indicate that further complexity in protein production may occur at the translational level. 2. Recent reports of “alternate” small sub-unit specificity affecting translation, - different eIs, - different small sub- - units.

36. What to Study? What regulates gene expression, How is gene expression modulated? –Transcriptionally, –Post-Transcriptionally, –Translationally.