1. MCB 7200: Molecular Biology Eukaryotic gene organization Restriction enzymes Cloning vectors

2. Eukaryotic gene organization Enhancers Silencers Insulators

3. Eukaryotic gene organization & RNA processing

4. Copyright © 2013 by W. H. Freeman and Company Molecular Cell Biology, 7 th Edition Lodish et al. Figure 4.15 Overview of RNA processing.

5. Copyright © 2013 by W. H. Freeman and Company Molecular Cell Biology, 7 th Edition Lodish et al. Figure 4.14 Structure of the 5’ methylated cap.

6. Basic Transcriptional Mechanisms and mRNA Splicing Animations MCB Chapter 4-Basic Molecular Genetic Mechanisms (animations) Life Cycle of mRNA  http://bcs.whfreeman.com/lodish7e/#800911__812036__ http://bcs.whfreeman.com/lodish7e/#800911__812036__ Basic Transcriptional Mechanisms  http://bcs.whfreeman.com/lodish7e/#800911__812037__ http://bcs.whfreeman.com/lodish7e/#800911__812037__ MCB Chapter 8-Post-transcriptional Gene Control (animation) mRNA Splicing  http://bcs.whfreeman.com/lodish7e/#800911__812057__ http://bcs.whfreeman.com/lodish7e/#800911__812057__

7. Copyright © 2013 by W. H. Freeman and Company Molecular Cell Biology, 7 th Edition Lodish et al. Figure 4.11 Three stages in transcription.

8. Prokaryotic vs. eukaryotic gene organization

9. Alternative splicing of eukaryotic 1° RNA transcripts

10. Eukaryotic gene expression

11. MCB Chapter 4-Life Cycle of mRNA MCB Chapter 4-Basic Molecular Genetic Mechanisms (animation) Life Cycle of mRNA  http://bcs.whfreeman.com/lodish7e/#800911__812036__ http://bcs.whfreeman.com/lodish7e/#800911__812036__

12. MCB Chapter 7-Yeast Two Hybrid System (exploiting transcriptional activators) MCB Chapter 7-Transcriptional Control of Gene Expression (animation) Yeast Two-Hybrid System  http://bcs.whfreeman.com/lodish7e/#800911__812055__ http://bcs.whfreeman.com/lodish7e/#800911__812055__

13. Insulators Two kinds of insulator functions. (A) Some insulators may function as barriers against the encroachment of adjacent genomic condensed chromatin. (B) Some insulators may serve as positional enhancer-blocking elements that prevent enhancer action when placed between enhancer and promoter, but not otherwise.

14. Copyright © 2013 by W. H. Freeman and Company Molecular Cell Biology, 7 th Edition Lodish et al. Experimental Figure 5.14 DNA cloning in a plasmid vector permits amplification of a DNA fragment. Recombinant DNA cloning procedure

15. MCB Chapter 5 - Molecular Genetic Techniques (animation) Plasmid Cloning  http://bcs.whfreeman.com/lodish7e/#800911__812047__ http://bcs.whfreeman.com/lodish7e/#800911__812047__

16. Restriction enzymes & DNA methylation

17. Recognition sequences of some REs EnzymeRecognition siteType of cut end EcoRI G ￬ A-A-T-T-C 5’ P extension BamHI G ￬ G-A-T-C-C 5’ P extension PstI C-T-G-C-A ￬ G 3’ P extension Sau3A1 ￬ G-A-T-C 5’ P extension PvuII C-A-G ￬ C-T-G Blunt end HpaI G-T-T ￬ A-A-C Blunt end HaeIII G-G ￬ C-C Blunt end NotI G ￬ C-G-G-C-C-G-C 5’ P extension

18. Mapping of restriction enzyme sites

19. Vector systemHost cellInsert capacity (kb) PlasmidE. coli0.1-10 Bacteriophage E. coli10-20 CosmidE. coli35-45 Bacteriophage P1E. coli80-100 BAC (bacterial artificial chromosome) E. coli50-300 P1 bacteriophage- derived AC E. coli100-300 YACYeast100-2,000 Human ACCultured human cells>2,000 Cloning vectors and their insert capacities

20. Copyright © 2013 by W. H. Freeman and Company Molecular Cell Biology, 7 th Edition Lodish et al. Figure 5.13 Basic components of a plasmid cloning vector that can replicate within an E. coli cell. 3 important features: Cloning site, Ori-an origin of replication, A selectable marker (amp r )

21. pBR322 The plasmid pBR322 is one of the most commonly used E.coli cloning vectors. pBR322 is 4361 bp in length and contains: (1) the replicon rep responsible for the replication of plasmid (source – plasmid pMB1); (2) rop gene coding for the Rop protein, which promotes conversion of the unstable RNA I – RNA II complex to a stable complex and serves to decrease copy number (source – plasmid pMB1); (3) bla gene, coding for beta-lactamase that confers resistance to ampicillin (source – transposon Tn3); (4) tet gene, encoding tetracycline resistance protein (source – plasmid pSC101). ori

22. pUC18/19 pUC18 and pUC19 vectors are small, high copy number, E.coli plasmids, 2686 bp in length. They are identical except that they contain multiple cloning sites (MCS) arranged in opposite orientations. pUC18/19 plasmids contain: (1) the pMB1 replicon rep responsible for the replication of plasmid (source – plasmid pBR322). The high copy number of pUC plasmids is a result of the lack of the rop gene and a single point mutation in rep of pMB1; (2) bla gene, coding for beta-lactamase that confers resistance to ampicillin (source – plasmid pBR322); (3) region of E.coli operon lac containing CAP protein binding site, promoter Plac, lac repressor binding site and 5’-terminal part of the lacZ gene encoding the N-terminal fragment of beta-galactosidase (source – M13mp18/19). This fragment, whose synthesis can be induced by IPTG, is capable of intra-allelic (alfa) complementation with a defective form of beta-galactosidase encoded by host (mutation lacZDM15). In the presence of IPTG, bacteria synthesize both fragments of the enzyme and form blue colonies on media with X-Gal. Insertion of DNA into the MCS located within the lacZ gene (codons 6-7 of lacZ are replaced by MCS) inactivates the N-terminal fragment of beta- galactosidase and abolishes alfa-complementation. Bacteria carrying recombinant plasmids therefore give rise to white colonies.pBR322M13mp18/19IPTGX-Gal

23. pGEM-3Z

24. Cloning foreign DNA into a plasmid vector Alkaline phosphatase-removes 5’ phosphate (P) groups of DNA molecules; BAP is more stable but less active than CIP T4 DNA ligase –joins 5’ phosphate (P) groups of DNA molecules to 3’ hydroxyl (OH) groups of DNA

25. Invitrogen’s Gateway® technology facilitates cloning of genes, into and out of, multiple vectors via site-specific recombination. Once a gene is cloned into an Entry clone you can then move the DNA fragment into one or more destination vectors simultaneously.

26. Some antibiotics commonly used as selective agents AntibioticDescription Ampicillin (Amp) Inhibits bacterial cell wall synthesis; inactivated by  - lactamase, which cleaves the  -lactam ring of amp Hygromycin B (HygB) Kanamycin (Kan)Binds to 30S ribosomal subunit and inhibits protein synthesis; inactivated by a phosphotransferase Neomycin (Neo)Binds to 30S ribosomal subunit and inhibits protein synthesis; inactivated by a phosphotransferase Streptomycin (Str) Tetracycline (Tet)Binds to 30S ribosomal subunit and inhibits protein synthesis; tet r gene encodes a protein which prevents transport of tet into the cell