AnnouncementsThis 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 theadditional 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

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:

(1) Each student enrolled in MCB 110L is responsible for all lecture material and lab experiments.

(2) If a lecture is missed or a lab is missed, there is no make-up for either.

(3) If an in-class pop quiz is missed, there is no make-up for the missed quiz.

(4) Missing a lecture or a lab also costs points in "lab management", which is 10% of your final grade.

(5) All experiments are conducted in teams of two; hence, your absence hurts your lab partner.

(6) 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.

(7) I hope you find the above information helpful in assisting you with scheduling your commitments this Spring Semester.

GRADING:

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

TOTAL 1,000

MCB 110L: Section I— The Power of Molecular GeneticsKeep your eyes on the prize: The objects of our focus for the next

five weeksGene Transcription by EukaryoticRNA Polymerase II

Initiation of mRNA Translationby Eukaryotic Ribosomes

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 interactionsbetween subunits (thickness of the connecting line represents the amount ofsurface area buried in the corresponding subunit interface) are depicted in theschematic diagram to the right. See: Cramer P, et al. (2001) Science 292: 1863-1876.

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 VLQEYRLTKQ1041 AFDWVLSNIE AQFLRSVVHP GEMVGVLAAQ SIGEPATQMT LNTFHFAGVA SKKVTSGVPR LKEILNVAKN MKTPSLTVYL1121 EPGHAADQEQ AKLIRSAIEH TTLKSVTIAS EIYYDPDPRS TVIPEDEEII QLHFSLLDEE AEQSFDQQSP WLLRLELDRA1201 AMNDKDLTMG QVGERIKQTF KNDLFVIWSE DNDEKLIIRC RVVRPKSLDA ETEAEEDHML KKIENTMLEN ITLRGVENIE1281 RVVMMKYDRK VPSPTGEYVK EPEWVLETDG VNLSEVMTVP GIDPTRIYTN SFIDIMEVLG IEAGRAALYK EVYNVIASDG1361 SYVNYRHMAL LVDVMTTQGG LTSVTRHGFN RSNTGALMRC SFEETVEILF EAGASAELDD CRGVSENVIL GQMAPIGTGA1441 FDVMIDEESL VKYMPEQKIT EIEDGQDGGV TPYSNESGLV NADLDVKDEL MFSPLVDSGS NDAMAGGFTA YGGADYGEAT1521 SPFGAYGEAP TSPGFGVSSP GFSPTSPTYS PTSPAYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP1601 TSPSYSPTSP SYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP1681 SYSPTSPSYS PTSPNYSPTS PSYSPTSPGY SPGSPAYSPK QDEQKHNENE NSR.

The RPO21 Gene Product (Rpo21)

CTD repeat: YSPTSPS

1 MTTQIRSPQG LPYPIQIDKL IPSVGSYLHE GDRLLVYKFW 41 YLVERASDTG DDDNEHDVSP GGSAGSNGVS PPTKQLRESI 81 EFFESPYEGD LISWNVDVGD EVATANQVIC EIKRPCNHDI121 VYGGLCTQCG KEVSADAFDG VPLDVVGDVD LQISETEAIR161 TGKALKEHLR RDKKLILVVD LDQTIIHCGV DPTIAEWKND201 PNNPNFETLR DVKSFTLDEE LVLPLMYMND DGSMLRPPPV241 RKCWYYVKVR PGLKEFFAKV APLFEMHIYT MATRAYALQI281 AKIVDPTGEL FGDRILSRDE NGSLTTKSLA KLFPTDQSMV321 VVIDDRGDVW NWCPNLIKVV PYNFFVGVGD INSNFLPKQS361 TGMLQLGRKT RQKSQESQEL LTDIMDNEKK LQEKIDKEVK401 RQEEKLNHQL ATAEEPPANE SKEELTKKLE YSASLEVQQQ441 NRPLAKLQKH LHDQKLLVDD DDELYYLMGT LSNIHKTYYD481 MLSQQNEPEP NLMEIIPSLK QKVFQNCYFV FSGLIPLGTD521 IQRSDIVIWT STFGATSTPD IDYLTTHLIT KNPSTYKARL561 AKKFNPQIKI VHPDWIFECL VNWKKVDEKP YTLIVDSPIS601 DEELQNFQTQ LQKRQEYLEE TQEQQHMLTS QENLNLFAAG641 TSWLNNDDDE DIPDTASDDD EDDDHDDESD DENNSEGIDR681 KRSIEDNHDD TSQKKTKAEP SQDGPVQHKG EGDDNEDSDS721 QLEEELMDML DD.

The FCP1 Gene Product (Fcp1)

BRCT domain

Halo-acid dehalogenase-

type phosphatase

domain