Prof. Jim Haber (email@example.com)
Dr. Sebastian Kadener (firstname.lastname@example.org)
Sept. 3 DNA fundamentals. (JEH)
Size of genomes, satellites, gene families, unique genes, cell constituents.
Sept. 7 Overview of Molecular Biology Tools and Techniques (JEH)
Southerns/Northerns, Libraries, cDNA, PCR, whole genome sequencing, from protein to gene
Sept. 10 Further Mol. Biol. Tools (JEH)
Gene modifications in vivo. (knock-outs, knock-ins, synthetic lethals). Epitope-tagging, Gene silencing methods (RNAi).
Sept. 14 Basic chromosome architecture (JEH)
Centromeres, telomeres and telomerase, isochores and gene distribution, "junk DNA"
Sept. 17 no class
Sept. 21 Basic chromatin (JEH)
The nucleosome, higher order structures, MNase and DNaseI protection,
acetylation, methylation, phosphorylation of histones
Sept. 24 Gene silencing (JEH)
Sir2 and the assembly of inactive chromatin. Telomere position effects and position effect variegation, Clr4/Swit6 assembly of heterochromatin.
Sept. 28 X chromosome inactivation and imprinting. (JEH)
Oct. 1 Microarrays and Genome-wide analysis of nucleic acids. (JEH)
Oct. 5 Hour and a half exam
Oct. 8 DNA replication 2 (JEH)
Genetic and biochemical strategies to understand DNA replication:
conditional mutants, synthetic lethal mutants, suppressors, two-hybrid and co-IP
Oct. 12 DNA replication 3 (JEH)
S phase and cell cycle regulation; licensing
Oct. 15 DNA repair and recombination (JEH)
Replication restart and recombination, break-induced replication and gene conversion
Oct. 19 DNA repair (JEH)
Mismatch repair, NER, bypass polymerases
Oct. 22 Transcription 1 (SK)
Polymerases, promoter structure, initiation site, PIC formation, holoenzyme
Oct. 29 Transcription 2 (SK)
TAFs, mechanisms of TAFs, upstream activators, enhancers, mediators, insulators
Nov. 2 Transcription 3 (SK)
Relationship to chromatin modification – insulators etc.
Nov. 5 Hour and a half exam
Nov. 9 RNA structure and function (SK)
Types of RNAs in the cell, stable RNAs, modified nucleotides, ribozymes.
Nov. 12 Splicing 1 (SK)
Types or RNA processing, intron/exon structure of genes, snRNPs, basic splicing mechanisms
Nov. 16 Splicing 2 (SK)
Alternative splicing, polyadenylation, RNA editing
Nov. 19 Splicing 3 (SK)
Interactions between transcription and splicing, i.e., connections between different steps.
Nov. 23 Analysis of protein complexes. (SK)
Two-hybrid, TAP-tagging, mass spec., protein complex mixtures and analysis of complexes.
Nov. 30 Ribosomes and protein synthesis (SK)
Dec. 3 Regulation of protein synthesis (SK)
Initiation, elongation, termination and miRNPs
Reading: Chapter 14-15
Dec. 7 RNA localization and relationship to translational control (SK)
Dec. 10 post-translational protein modification and protein turnover (SK)
Dec. 15 final exam 6pm
In addition to the sections of the “Watson” book, there will be a number of papers assigned for you to read, usually 1 or 2 per class. They will be discussed in class and you should be prepared to answer questions about them.
Lecture notes will be posted on the web usually after class.
If you have a documented learning disability and would like to have an accommodation made in taking this class, please let Prof. Haber know immediately.