REI4SED: $8 Dec 09

Biochemistry 8002Molecular Biology: The study of gene structure and function at the molecular level.

Fall 2009 Nl/W lF 9:05-9:5Sam MCB 2-t2O

Please note that the syllabus will be refined as the semester proceeds (changes/additions will be colored purplel.

Obiectives:To establish a deep basic understanding of the fundamental concepts and techniques of molecular biology. The course is alsodesigned to learn to criticaily analyze primary literature.

Course instructors:Dr. Kathleen Conklin (course directorJ Dr. Reuben HarrisGenetics, Cell Biology and Development (GCD) Biochemistry, Molecular Biology and Biophysics [BMBBj5-220 Moos Tower 6-104 MCBOffice hrs: TBA Office hrs: arrange by email: rsh@umn.edu

Teaching assistants:Mr. fudd Hultquist Ms. Lela LackeyGenetics, Cell Biology and Development (GCD) Biochemistry, Molecular Biology and Biophysics [BMBBJEmail: hultq014(aumn.edu Email: lackO052@umn.eduUofM-hardcopy assignments to Mr. Hultquist Office hours: B-9am, Wednesdays, MCB 6-118Duluth-email assignments to Mr. Hultquist

Textbook:"Molecular Biology: Genes to Proteins", 3'd ed, Burton E Tropp, fones and Bartlett Publisher, 2008

Evaluation:Final letter grades A-F will be determined based on the following:

1. 350/o Harris section: l-pt participation; 10pt gene illustration assignment; 3Opt gene cloning & expressing assignment.2. 350/o Conklin section.3. 300/o Cumulative final exam.

LEC DATE DAY INSTR TOPIC/READING ASSIGNMENT/TECHNIOUE1 9-9 W RH-1 Introduction - Topic 1: Practical molecular biology: cloning a GOI

. Tropp Chapters 1,2,3 &5r NEB cataloss

2 9-L7 F RH-2 Topic 1 contd': Template identification and acquisitionTake-home assignment (10pts); Due 9/14 before class

3 9-1.4 M RH.3 Topic L contd': Vector selection and preparation4 9-L6 W RH.4 Topic 1 contd': Ligation, restriction, and DNA sequencing5 9-18 F RH.5 Topic 1 contd': Functional verification

Take-home assisnment f3Opts); Due9/23 before class6 9-27 M RH.5 Topic 2: SV40 large T antigen, p53, and eukaryotic DNA replication

. Tropp Chapters 4,6,8 &9

. Review: Fanning E, Zhao K. (2009) SV40 DNA replication: from the A gene to a

nanomachine. Virology 384(2):352-9.e Article: Melendy T, Stillman B, [1993) An interaction between replication

protein A and SV40 T antigen appears essential for primosome assembly duringSV40 DNA replication. T Biol Chem. 268f51:3389-95.

7 9-23 W RH-7 Topic 2 contd': discussion and short group presentations8 9-25 F RH.B Topic 2 contd': discussion and short group presentations

In class quiz or take home assisnment to be announced9 9-28 M RH-9 Topic 3: HIV-1Vif, APOBEC3G, retrovirus replication & mutation

. Tropp Chapters 1, B & 10r Review: Malim & Emerman [2008) HIV-1 accessory proteins--ensuring viral

survival in a hostile environment. Cell Host & Microbe 3, 3BB-98.r Article: Harris ef al (2003) DNA deamination mediates innate immunity to

retroviral infection. Cell 113, 803-9.t0 9-30 W RH-10 Topic 3 contd': discussion and short group presentationsl1 10-2 F RH-11 Topic 3 contd': discussion and short group presentations

In class ouizL2 10-5 M RH-12 Topic 4: Adenovirus replication & recombination

r Tropp Chapter B & 11

fuE\/ISED: $8 Dec 09

r Review: Weitzman et al (2004) Interactions of viruses with the cellular DNArepair machinery. DNA repair 3, 7765-73.

r Article: Stracker, Carson & Weitzman (2002) Adenovirus oncoproteinsinactivate the Mre11-Rads0-NBS1 DNA repair complex. Nature 41,8,348-52.

13 t0-7 W RH-13 Topic 4 contd': discussion and short group presentationsTake-home assignment to be announced

l4 10-9 F KC-1 RNA Polymerases I and III; Function and Regulationr Tropp Ch 18r Review: White, RJ. RNA polymerases I and III, growth control and cancer. Nat

Rev Mol Cell Biol. 2005.6(1\69-78.15 70-12 M KC-2 Article for discussion: Grandori C, Gomez-Roman N, Felton-Edkins ZA, Ngouenet C,

Galloway DA, Eisenman RN, White RJ. c-Myc binds to human ribosomal DNA andstimulates transcription of rRNA genes by RNA polymerase I. Nat Cell Biol. 2005Mar;713.):311-8.

L6 10-t4 KC-3 mRNA Processing I: Splicing and Alternative Splicing and RNA editing. Tropp Ch 17o Review: WangZ, Burge CB. Splicing regulation: from a parts list of regulatory

elements to an integrated splicing code. RNA. 2008 Mav;14[5]:802-13.L7 10-16 F KC-4 Article for discussion: Anquetil V, Le Sommer C, M6reau A, Hamon S, Lerivray H, Hardy S.

The polypyrimidine tract binding protein (PTB) prevents the activity of an intronicregulatory element that promotes the usage of a composite 3' terminal exon. J Biol Chem.2009 Sep 17. [Epub ahead ofprintl

1B 10-19 M KC-5 mRNA Processing II: 5' and 3'processing [capping and polyadenylationJ. Tropp Ch 17

L9 70-27 W KC-6 Article for discussion: Widespread shortening of 3'UTRs by alternative cleavage andpolyadenylation activates oncogenes in cancer cells. Mayr C, Bartel DP Cell. 2009 Aug21:138($:673-84.

20 L0-23 F KC-7 mRNA Export and Localization. Tropp Ch 17o Review: mRNA localization: gene expression in the spatial dimension. Martin KC,

Ephrussi A. Ce11. 2009 Feb 20;136(4):719-30.r Review: mRNA nuclear export at a glance. Carmody SR, Wente SR. J Cell Sci. 2009

I un I 5 ;122(P t l2): 1933 -7 .

27 70-26 M KC-B Assisnment on mRNA localization22 70-28 W KC.9 Co-ordination of Postranscriptional Events

. Tropp Ch 17r Review: "Cotranscriptionality": the transcription elongation complex as a nexus for

nuclear ffansactions. Perales R, Bentley D. Mol Cell. 2009 Oct 23:36(2):l'78-91 .

LJ 10-30 F KC-10 Article for discussion: Recruitment of P-TEFb (Cdk9-Pch1) to chromatin by the cap-methyltransferase Pcml in fission yeast. Guiguen A, Soutourina J, Dewez M, Tafforeau L, Dieu M,Raes M. Vandenhaute J. Werner M. Hermand D. EMBO J.2007 Mar 2l:266):1552-9.

24 11-2 M RH-14 Topic 5: Gene therapy & methods to cure disease. Tropp Chapter 11. Review: Porteus & Carroll (2005] Gene targeting using zinc finger nucleases.

Nature Biotech,r Article: Perez et al (2008) Establishment of HIV-L resistance in CD4+ T cells by

genome editing using zinc-finger nucieases. Nature Biotech 26,808-1.6.Special event: Dr. Paula Cannon, MICaB invited seminar speaker, noon. To view:httos : / /umconnect.umn.edu / o19258597 /

25 t7-4 w RH-15 Topic 5 contd': discussion and short group presentations26 1,1-6 F RH-16 Topic 5 contd': discussion and short group presentations

In class ouiz27 LL-9 M RH-17 Topic 6 - Telomerase, HTLV & Cancer (T.A. choice)

. Tropp Chapter sections 6.5 and 9.9r Review: Bellon & Nicot (2008) INCI 100, 9B-108r Article 1. Gabet et al (2003) Oncogene 22,3734-37 4I.r Article 2. Sinha-Datta et al [2004) Blood 104, 2523-2537.. Supplement: TMP assay: Fajkus [2006) CCA. Supplement: Tropp Chapters 15 & 16 lPol II transcriotionl

2B 17-11 W RH.1B Tooic 5 contd'29 17-13 F RH-19

Take home assignment (15pts; due lL/L6 before class)(questions are on the final slide of the powerDoint)

Topic 6 contd'

REI4SED: A8 Dec {)9

30 t1,-16 M RH-20 Topic 6 contd': open discussionReview session and instructor evaluation

31 11-18 W KC-11 Translational Regulation: Initiation and Recruitment to polysomesr Trooo Ch2.1.2.2:20

JL 11,-20 F KC.12 Article for discussion I: Loss-of-function mutations of an inhibitory upstream 0RF in thehuman hairless transcript cause Marie Unna hereditary hypotrichosis. Wen Y, et al. NatGenet. 2 009 F eb; 47( 2) :228-33.

.l -1 L1,-23 M KC-13 Article for discussion II: The splicing factor SFZ/ASF regulates translation initiation byenhancing phosphorylation of 4E-BP1. Michlewski G, Sanford f R, Ciiceres JF, Mol Cell.2008 Aor 25:30(2):17 9-89.

34 t7-25 W KC-74 mRNA stability: Regulation and Quality Control Pathwaysr Review: The highways and byways of mRNA decay. Garneau NL, et al. Nat Rev

Mol Cell Biol. 2007 Feb;B(2):713-26.o Review: Early nonsense: mRNA decay solves a translational problem, Amrani N,

Sachs MS, Tacobson A. Nat Rev Mol Cell Biol. 2006 lun:7161:415-25.LT-27 F THANKSGIVING HOLIDAY

35 11-30 M KC-15 Article for discussion: Ultraconserved elements are associated with homeostatic controlof splicing regulators by alternative splicing and nonsense-mediated decay. Ni lZ, et al.Genes Dev. 2007 Mar t5;21(6):708-L8.

36 12-2 KC-16 Post-translational modifications: Types and outcomesr Review: Ubiquitin and ubiquitin-like proteins as multifunctional signals.

Welchman RL, Gordon C, Mayer RJ. Nat Rev Mol Cell Biol. 2005 Aug;6(B):599-609.

J/ 72-4 F KC-17 Article for discussion: The ubiquitin-specific protease USP2B is required for MYC stability.Popov N, et al. Nat Ce]] Biol. 2007 lul;9(7):7 65-7 4.

38 12-7 M KC-18 Small/non-coding RNAs: experimental and endogenousr Review: Many roads to maturity: microRNA biogenesis pathways and their

regulation. Winter J, et al. Nat Cell Biol. 2009 Mar;11(3):228-34.. Review: Small silencing RNAs: an expanding universe. Ghildiyal M, Zamore PD,

Nat Rev Genet. 2009 Feb:10f21:94-108.39 12-9 W KC.19 Article for discussion I: Redirection ofsilencing targets by adenosine-to-inosine editing of

miRNAs. Kawahara Y, et al. Science. 2007 Feb 23;315(5815):1137-40.40 12-11 F KC-20 Article for discussion II: miR-145 and miR-143 regulate smooth muscle cel1 fate and

plasticitv. Cordes KR, et al. Nature. 2009 Aue 6'.460(7256\:705-10.41 t2-74 M KC-27 OPEN REVIEW SESSION

42 t2-16 W FINAL EXAM

Other Important Information:

Electronic Devices: No electronic devices of any kind,examinations. Use of a prohibited dl2evice duringUniversity Student Conduct Code.

including computers, calculators, iPods, oran examination is considered Scholastic

REI4SED: 08 Dec {)9

cell phones, may be used duringDishonesty and falls under the

Make up Exams: Requests for make up exams should be made only under extremely unusual circumstances and will be granted atthe discretion of the instructors.

Academic Misconduct: Violations of acceptable academic conduct will elicit penalties such as a failing grade for the examination ora failing grade for the entire course, depending upon the nature and severity of the infraction. Although collaboration duringexaminations is strictly forbidden, students may work together on problem sets if the instructor gives explicit permission.

Academic lntegriU: The grade in a course is intended to be a reflection of what you have learned in the course. Any instances ofplagiarism [presenting someone else's work as your own) will be dealt with through university procedures for academicdishonesty (see Student fudicial Affairs for more information: http://www.sja.umn.edu/ ). If you need assistance in distinguishingbetween plagiarism and legitimate use and citation of someone else's work, please refer tohttp://CISW.cla.umn.edu/ugradinfo.html <http://CISW.cla.umn.edu/ueradinfo.html> and talk to the course instructor.