Announcements This course is MCB 110L Prerequisites :

1. Announcements This course is MCB 110L Prerequisites: BMB, Track 1: MCB C100A; MCB 100B; MCB 110 (may be taken concurrently) BMB, Track 2: MCB C100A; Chem. 135; MCB 110 (may be taken concurrently) Chem. Bio.: Chem. C130-130B (or Chem. 120A-120B); Chem. 135; MCB 110 (may be taken concurrently) Lab Manual: Purchase ASAP at Copy Central, 48 Shattuck Square Required Reading for Lecture #1: Short article by Botstein & Fink Additional Required Reading: Each experimental protocol and the additional background articles by Sherman in the Lab Manual Exam Date: FRIDAY, 22 February 2008 Course Policies: READ THE HANDOUT (& remember its content) Pre-lab Safety Lecture (~15 min): Ann Fischer BMB Laboratories Supervisor

2. For those of you who are already planning your post-Cal life, and arranging for career-related interviews (e.g., at medical schools, graduate schools, pharmacy schools, optometry schools, veterinary schools, pharmaceutical companies, biotech firms, etc. etc.), please keep in mind that: Each student enrolled in MCB 110L is responsible for all lecture material and lab experiments. If a lecture is missed or a lab is missed, there is no make-up for either. If an in-class pop quiz is missed, there is no make-up for the missed quiz. Missing a lecture or a lab also costs points in "lab management", which is 10% of your final grade. All experiments are conducted in teams of two; hence, your absence hurts your lab partner. The instructor may consider imposing an additional penalty for any unexcused absence from lecture or lab (such as completion of an additional relevant assignment outside of class). See: MCB 110L Policy Statement for definition and discussion of excused absences. I hope you find the above information helpful in assisting you with scheduling your commitments this Spring Semester.

3. GRADING: Five lab reports at 100 pts. per report = 500 Flowcharts for 5 exps. at 20 pts. per chart = 100 Occasional in-class pop quizzes = 100 General lab management and decorum = 100 End-of-Section I Examination = 200 TOTAL 1,000

4. Keep your eyes on the prize: The objects of our focus for the next five weeks Gene Transcription by Eukaryotic RNA Polymerase II Initiation of mRNA Translation by Eukaryotic Ribosomes MCB 110L: Section I— The Power of Molecular Genetics

5. Ribbon diagram of the structure of yeast RNA polymerase II at 2.8 Å resolution. Identity and location of each of the ten subunits is color-coded and interactions between subunits (thickness of the connecting line represents the amount of surface area buried in the corresponding subunit interface) are depicted in the schematic diagram to the right. See: Cramer P, et al. (2001) Science 292: 1863-1876.

6. 1 MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS IDRNLKCQTC QEGMNECPGH 81 FGHIDLAKPV FHVGFIAKIK KVCECVCMHC GKLLLDEHNE LMRQALAIKD SKKRFAAIWT LCKTKMVCET DVPSEDDPTQ 161 LVSRGGCGNT QPTIRKDGLK LVGSWKKDRA TGDADEPELR VLSTEEILNI FKHISVKDFT SLGFNEVFSR PEWMILTCLP 241 VPPPPVRPSI SFNESQRGED DLTFKLADIL KANISLETLE HNGAPHHAIE EAESLLQFHV ATYMDNDIAG QPQALQKSGR 321 PVKSIRARLK GKEGRIRGNL MGKRVDFSAR TVISGDPNLE LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP 401 GAKYVIRDSG DRIDLRYSKR AGDIQLQYGW KVERHIMDND PVLFNRQPSL HKMSMMAHRV KVIPYSTFRL NLSVTSPYNA 481 DFDGDEMNLH VPQSEETRAE LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKLTLRDTF IELDQVLNML YWVPDWDGVI 561 PTPAIIKPKP LWSGKQILSV AIPNGIHLQR FDEGTTLLSP KDNGMLIIDG QIIFGVVEKK TVGSSNGGLI HVVTREKGPQ 641 VCAKLFGNIQ KVVNFWLLHN GFSTGIGDTI ADGPTMREIT ETIAEAKKKV LDVTKEAQAN LLTAKHGMTL RESFEDNVVR 721 FLNEARDKAG RLAEVNLKDL NNVKQMVMAG SKGSFINIAQ MSACVGQQSV EGKRIAFGFV DRTLPHFSKD DYSPESKGFV 801 ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK 881 QSLDTIGGSD AAFEKRYRVD LLNTDHTLDP SLLESGSEIL GDLKLQVLLD EEYKQLVKDR KFLREVFVDG EANWPLPVNI 961 RRIIQNAQQT FHIDHTKPSD LTIKDIVLGV KDLQENLLVL RGKNEIIQNA QRDAVTLFCC LLRSRLATRR VLQEYRLTKQ 1041 AFDWVLSNIE AQFLRSVVHP GEMVGVLAAQ SIGEPATQMT LNTFHFAGVA SKKVTSGVPR LKEILNVAKN MKTPSLTVYL 1121 EPGHAADQEQ AKLIRSAIEH TTLKSVTIAS EIYYDPDPRS TVIPEDEEII QLHFSLLDEE AEQSFDQQSP WLLRLELDRA 1201 AMNDKDLTMG QVGERIKQTF KNDLFVIWSE DNDEKLIIRC RVVRPKSLDA ETEAEEDHML KKIENTMLEN ITLRGVENIE 1281 RVVMMKYDRK VPSPTGEYVK EPEWVLETDG VNLSEVMTVP GIDPTRIYTN SFIDIMEVLG IEAGRAALYK EVYNVIASDG 1361 SYVNYRHMAL LVDVMTTQGG LTSVTRHGFN RSNTGALMRC SFEETVEILF EAGASAELDD CRGVSENVIL GQMAPIGTGA 1441 FDVMIDEESL VKYMPEQKIT EIEDGQDGGV TPYSNESGLV NADLDVKDEL MFSPLVDSGS NDAMAGGFTA YGGADYGEAT 1521 SPFGAYGEAP TSPGFGVSSP GFSPTSPTYS PTSPAYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP 1601 TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP 1681 SYSPTSPSYS PTSPNYSPTS PSYSPTSPGY SPGSPAYSPK QDEQKHNENE NSR. The RPO21 Gene Product (Rpo21) CTD repeat: YSPTSPS

10. The FCP1 Gene Product (Fcp1) 1 MTTQIRSPQG LPYPIQIDKL IPSVGSYLHE GDRLLVYKFW 41 YLVERASDTG DDDNEHDVSP GGSAGSNGVS PPTKQLRESI 81 EFFESPYEGD LISWNVDVGD EVATANQVIC EIKRPCNHDI 121 VYGGLCTQCG KEVSADAFDG VPLDVVGDVD LQISETEAIR 161 TGKALKEHLR RDKKLILVVD LDQTIIHCGV DPTIAEWKND 201 PNNPNFETLR DVKSFTLDEE LVLPLMYMND DGSMLRPPPV 241 RKCWYYVKVR PGLKEFFAKV APLFEMHIYT MATRAYALQI 281 AKIVDPTGEL FGDRILSRDE NGSLTTKSLA KLFPTDQSMV 321 VVIDDRGDVW NWCPNLIKVV PYNFFVGVGD INSNFLPKQS 361 TGMLQLGRKT RQKSQESQEL LTDIMDNEKK LQEKIDKEVK 401 RQEEKLNHQL ATAEEPPANE SKEELTKKLE YSASLEVQQQ 441 NRPLAKLQKH LHDQKLLVDD DDELYYLMGT LSNIHKTYYD 481 MLSQQNEPEP NLMEIIPSLK QKVFQNCYFV FSGLIPLGTD 521 IQRSDIVIWT STFGATSTPD IDYLTTHLIT KNPSTYKARL 561 AKKFNPQIKI VHPDWIFECL VNWKKVDEKP YTLIVDSPIS 601 DEELQNFQTQ LQKRQEYLEE TQEQQHMLTS QENLNLFAAG 641 TSWLNNDDDE DIPDTASDDD EDDDHDDESD DENNSEGIDR 681 KRSIEDNHDD TSQKKTKAEP SQDGPVQHKG EGDDNEDSDS 721 QLEEELMDML DD. Halo-acid dehalogenase-type phosphatase domain BRCT domain