1. MCB 720: Molecular Biology Eukaryotic gene organization Restriction enzymes Cloning vectors

2. Eukaryotic gene organization enhancers silencers

3. Eukaryotic gene organization & RNA processing

4. Basic Transcriptional Mechanism and mRNA Splicing Animations MCB Chapter 4-Basic Transcriptional Mechanism animation http://bcs.whfreeman.com/lodish5e/pages/bcs- main.asp?v=category&s=00010&n=04000&i=04010.01&o=|00510|00610| 00520|00530|00540|00560|00570|00590|00600|00700|00710|00010| 00020|00030|00040|00050|01000|02000|03000|04000|05000|06000| 07000|08000|09000|10000|11000|12000|13000|14000|15000|16000| 17000|18000|19000|20000|21000|22000|23000|99000|&ns=0 http://bcs.whfreeman.com/lodish5e/pages/bcs- main.asp?v=category&s=00010&n=04000&i=04010.01&o=|00510|00610| 00520|00530|00540|00560|00570|00590|00600|00700|00710|00010| 00020|00030|00040|00050|01000|02000|03000|04000|05000|06000| 07000|08000|09000|10000|11000|12000|13000|14000|15000|16000| 17000|18000|19000|20000|21000|22000|23000|99000|&ns=0 MCB Chapter 12-mRNA splicing animation http://bcs.whfreeman.com/lodish5e/pages/bcs- main.asp?v=category&s=00010&n=12000&i=12010.02&o=|00510|00610| 00520|00530|00540|00560|00570|00590|00600|00700|00710|00010| 00020|00030|00040|00050|01000|02000|03000|04000|05000|06000| 07000|08000|09000|10000|11000|12000|13000|14000|15000|16000| 17000|18000|19000|20000|21000|22000|23000|99000|&ns=1211 http://bcs.whfreeman.com/lodish5e/pages/bcs- main.asp?v=category&s=00010&n=12000&i=12010.02&o=|00510|00610| 00520|00530|00540|00560|00570|00590|00600|00700|00710|00010| 00020|00030|00040|00050|01000|02000|03000|04000|05000|06000| 07000|08000|09000|10000|11000|12000|13000|14000|15000|16000| 17000|18000|19000|20000|21000|22000|23000|99000|&ns=1211

5. Prokaryotic vs. eukaryotic gene organization

6. Alternative splicing of eukaryotic 1° RNA transcripts

7. Eukaryotic gene expression

8. MCB Chapter 4-Life Cycle of mRNA http://bcs.whfreeman.com/lodish5e/pages/bcs- main.asp?v=category&s=00010&n=04000&i=04010.02&o=|0 0510|00610|00520|00530|00540|00560|00570|00590|006 00|00700|00710|00010|00020|00030|00040|00050|01000 |02000|03000|04000|05000|06000|07000|08000|09000|1 0000|11000|&ns=0 http://bcs.whfreeman.com/lodish5e/pages/bcs- main.asp?v=category&s=00010&n=04000&i=04010.02&o=|0 0510|00610|00520|00530|00540|00560|00570|00590|006 00|00700|00710|00010|00020|00030|00040|00050|01000 |02000|03000|04000|05000|06000|07000|08000|09000|1 0000|11000|&ns=0

9. MCB Chapter 11-Yeast Two Hybrid System (exploiting transcriptional activators) http://bcs.whfreeman.com/lodish5e/pages/bcs- main.asp?v=category&s=00010&n=11000&i=11010.01&o=|0 0510|00610|00520|00530|00540|00560|00570|00590|006 00|00700|00710|00010|00020|00030|00040|00050|01000 |02000|03000|04000|05000|06000|07000|08000|09000|1 0000|11000|&ns=798 http://bcs.whfreeman.com/lodish5e/pages/bcs- main.asp?v=category&s=00010&n=11000&i=11010.01&o=|0 0510|00610|00520|00530|00540|00560|00570|00590|006 00|00700|00710|00010|00020|00030|00040|00050|01000 |02000|03000|04000|05000|06000|07000|08000|09000|1 0000|11000|&ns=798

10. Recombinant DNA cloning procedure

11. See MCB Chapter 9 – Plasmid Cloning http://bcs.whfreeman.com/lodish5e/pages/bcs- main.asp?v=category&s=00010&n=09000&i=09010.05&o=|0 0510|00610|00520|00530|00540|00560|00570|00590|006 00|00700|00710|00010|00020|00030|00040|00050|01000 |02000|03000|04000|05000|06000|07000|08000|09000|1 0000|11000|&ns=437 http://bcs.whfreeman.com/lodish5e/pages/bcs- main.asp?v=category&s=00010&n=09000&i=09010.05&o=|0 0510|00610|00520|00530|00540|00560|00570|00590|006 00|00700|00710|00010|00020|00030|00040|00050|01000 |02000|03000|04000|05000|06000|07000|08000|09000|1 0000|11000|&ns=437

12. Restriction enzymes & DNA methylation

13. 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

14. Mapping of restriction enzyme sites

15. 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

16. Plasmid cloning vectors Three important features 1.Cloning site 2.Ori-an origin of replication 3.A selectable marker (amp r )

17. 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

18. 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

19. pGEM-3Z

20. 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

21. 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