MBIOL 395J

Spring 2009

Instructors:

TA:

Lecture Room and Time:

Class materials

Syllabus

Helpful Hints for Succeeding in 395J

Note about textbook reading: Most of the figures Dr. Molineux presents in class are in your textbook. Read the material relevant to these figures. If there is extra reading required from the text, we will let you know.

Tues 1-20	Lecture 1: DNA/RNA structure Readings: Advances in mechanisms of genetic instability related to hereditary neurological diseases Non-B DNA Conformations, Genomic Rearrangements, and Human Disease The involvement of non-B DNA structures in gross chromosomal rearrangements The triple helix: 50 years later, the outcome Molecular Structure of Nucleic Acids Z-DNA-forming sequences generate large-scale deletions in mammalian cells
Th 1-22	Lecture 2: DNA/RNA structure continued Readings: Base-stacking and base-pairing contributions into thermal stability of the DNA double helix Supercoiling of DNA <-- A helpful set of notes DNA TOPOISOMERASES: Structure, Function,and Mechanism Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
Tues 1-27	Lecture 3: DNA Replication Readings: Dividing the workload at a eukaryotic replication fork The Chromosome Replication Machinery of the Archaeon Sulfolobus solfataricus Replisome mechanics: insights into a twin DNA polymerase machine
Th 1-29	Lecture 4: DNA Replication
Tu 2-3	Lecture 5: DNA Replication and Replication Initiation, Bonus Content: DNA Repair Readings: DNA replication initiation: mechanisms and regulation in bacteria Once in a lifetime: strategies for preventing re-replication in prokaryotic and eukaryotic cells
Th 2-5	Lecture 6: DNA Repair
Tu 2-10	Lecture 7: DNA Repair and Associated Recombination Readings: Mechanistic flexibility as a conserved theme across 3 billion years of NHEJ Paradigms for the Three Rs: DNA Replication, Recombination, and Repair RNA polymerase: The most specific damage recognition protein in cellular responses to DNA damage? Transcription-coupled DNA repair: two decades of progress and surprises
Th 2-12	Lecture 8: DNA Recombination Reading: Connecting Replication and Recombination ERROR-PRONE REPAIR DNA POLYMERASES IN PROKARYOTES AND EUKARYOTES Substrate Specificity of RusA Resolvase Reveals the DNA Structures Targeted by RuvAB and RecG In Vivo Unity in transposition reactions
Tu 2-17	Lecture 9: Chromatin Structure Readings: Genome-Scale Identification of Nucleosome Positions in S. cerevisiae X-ray structure of a tetranucleosome and its implications for the chromatin fibre The DNA-encoded nucleosome organization of a eukaryotic genome
Th 2-19	EXAM I Key and Grade Spread Practice Exam Practice Exam Key
Tu 2-24	Lecture 10: Transcription Mechanism Readings: Bacterial RNA Polymerases: The Wholo Story RNA Polymerase I: A Multifunctional Molecular Machine A Long Time in the Making— The Nobel Prize for RNA Polymerase The molecular basis of eukaryotic transcription
Th 2-26	Lecture 11: Transcription Mechanism continued Readings: Intrinsic Termination and Anti-termination Regulatin' RNAP through the Secondary Channel- GreA and B
Tu 3-3	Lecture 12: Prokaryotic Transcription Regulation Readings: General Pathway for Turning on Promoters Transcribed by RNA Polymerases Containing Alternative Sigma Factors How do site-specifc DNA-binding proteins find their targets? Regulation by destruction: design of the sE envelope stress response
Th 3-5	Lecture 13: Operons and Regulons Readings: Maturation and degradation of RNA in bacteria
Tu 3-10	Lecture 14: Operons and Regulons + RNA Processing
Th 3-12	Exam II Exam II Key
March 16-20	SPRING BREAK, Woo Hoo!!
Tu 3-24	Lecture 15: Eukaryotic Transcription machinary Readings: Structure and Mechansism of RNAPII Machinery Factors Involved in Specific Transcription by Mammalian RNA Polymerase II: Role of Transcription Factors IIA, IID, and IIB during Formation of a Transcription-Competent Complex Structural Basis of Transcription: Separation of RNA from DNA by RNA Polymerase II
Th 3-26	Lecture 16: Eukaryotic transcriptional regulation, chromatin remodeling Reading: Regulation of RNA Polymerase II Transcription by Sequence-Specific DNA Binding Factors Insulators: exploiting transcriptional and epigenetic mechanisms Transcriptional Activation by Recruitment Generation and Interconversion of Multiple Distinct Nucleosomal States as a Mechanism for Catalyzing Chromatin Fluidity
Tu 3-31	Lecture 17: RNA processing: Capping, 3´-end formation, RNA editing Readings: Molecular Architecture of the Human Pre-mRNA 30 Processing Complex Pre-mRNA Processing Reaches Back to Transcription and Ahead to Translation Processing the message: structural insights into capping and decapping mRNA The RNA world meets behavior:AfiI pre-mRNA editing in animals RNA editing in regulating gene expression in the brain
Th 4-2	Lecture 18: Pre-mRNA splicing mechanisms, alternative splicing Readings: The Spliceosome: Design Principles of a Dynamic RNP Machine RS domains contact the pre-mRNA throughout spliceosome assembly Mutually Exclusive Splicing of the Insect Dscam Pre-mRNA Directed by Competing Intronic RNA Secondary Structures Alternative pre-mRNA splicing: the logic of combinatorial control Cryo-Electron Microscopy of Spliceosomal Components
Tu 4-7	Lecture 19: Catalytic RNAs: Self-splicing introns and ribozymes Readings: The natural history of group I introns Ribozyme mechanisms and folding Ribozyme Catalysis of Metabolism in the RNAWorld Homing endonuclease structure and function
Th 4-9	Lecture 20: RNA transport and localization Reading: mRNA Localization: Gene Expression in the Spatial Dimension Exporting RNA from the nucleus to the cytoplasm The Glc7p Nuclear Phosphatase Promotes mRNA Export by Facilitating Association of Mex67p with mRNA From Birth to Death: The Complex Lives of Eukaryotic mRNAs PLEASE NOTE: You might see an error when opening this paper ("Insufficient data to open the picture" or something like this), please ignore this. It doesnt pertain to any of the paper information, only the cover page (which you dont need).
Tu 4-14	Exam III Practice Exam from 2008 with Key Exam III Key + Grade Stats
Th 4-16	Lecture 21: Ribosome structure and assembly Readings: The accuracy of ribosomal RNA comparative structure models Structure and Function of Escherichia coli Ribosomes An assembly landscape for the 30S ribosomal subunit Crystal Structure of the Ribosome at 5.5 � Resolution A hierarchical model for evolution of 23S ribosomal RNA
Tu 4-21	Lecture 22: Translation: Initiation and control Readings: Where to begin? The mechanism of translation initiation codon selection in eukaryotes Structural and mechanistic insights into hepatitis C viral translation initiation Complex Riboswitches
Th 4-23	Lecture 23: Translation: Elongation and termination Reading: Trans-Translation: The tmRNA-Mediated Surveillance Mechanism for Ribosome Rescue, Directed Protein Degradation, and Nonstop mRNA Decay A structural understanding of the dynamic ribosome machine
Tu 4-28	Lecture 24: Eukaryotic RNA Turnover Readings: The enzymes and control of eukaryotic mRNA turnover Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex Ccr4p is the catalytic subunit of a Ccr4p/Pop2p/Notp mRNA deadenylase complex in Saccharomyces cerevisiae
Th 4-30	Lecture 25: Protein turnover Readings: PROTEASOMES AND THEIR KIN: PROTEASES IN THE MACHINE AGE Back to the Future with Ubiquitin The N-end rule: Functions, mysteries, uses Proposed role of ATP in protein breakdown: Conjugation of proteins with multiple chains of the polypeptide of ATP-dependent proteolysis
Tu 5-5	LAST LECTURE!! Lecture 23: Functions of ncRNA in gene expression: siRNA, miRNA and others Readings: Potent and specific genetic interference by double-strandedRNA in Caenorhabditis elegans MicroRNAs: Genomics, Biogenesis, Mechanism, and Function Origins and Mechanisms of miRNAs and siRNAs
Th 5-7	EXAM IV Practice Exam from 2008 with Key 2009 Key with Stats

Mol 190 (Only required for ICMB students, although other 395J students are encouraged to attend) Mon 1:30pm @ MBB 1.210

***Please remember that participation will count toward your grade, so come prepared with questions for the presenters. Also note that we will be keeping attendance.***

One thing to note regarding journal club: Please don't hesitate to site and bring in data from other papers that may strengthen the conclusions of the core paper. It is useful to see that other scientists may reach the same results with different experiments. Additionally, the focus isn't always just the results of the data, but also the experiments themselves. If interesting or clever experiments were performed, make note of them; they might be useful to all of us.

SCHEDULE:

DATE

PRESENTERS

READING

1-26

Orginizational Meeting-

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2-2

Dynamics of DNA replication loops reveal temporal
control of lagging-strand synthesis

2-9

Division of Labor at the Eukaryotic Replication Fork

2-16