Biology 105b     Molecular Biology

 

Prof.  Jim Haber (haber@brandeis.edu)

Dr. Sebastian Kadener (skadener@brandeis.edu)

 

See also http://www.bio.brandeis.edu/classes/biol105/   

 

TA   Jamie Foti (foti@brandeis.edu)

 

Syllabus

 

Sept. 3  DNA fundamentals.  (JEH)

Size of genomes, satellites, gene families, unique genes, cell constituents.

Reading:  Watson et al. Molecular Biology of the Gene 5th Edition    Chapters 1-5 are useful background.  Chapter 6 concerning DNA structure

 

Sept. 7  Overview of Molecular Biology Tools and Techniques  (JEH)

Southerns/Northerns, Libraries, cDNA, PCR, whole genome sequencing, from protein to gene

Reading:  Chapter 20

 

Sept. 10  Further Mol. Biol. Tools  (JEH)

Gene modifications in vivo. (knock-outs, knock-ins, synthetic lethals).  Epitope-tagging,  Gene silencing methods (RNAi). 

Reading:  Chapter 20

 

Sept. 14  Basic chromosome architecture (JEH)

Centromeres, telomeres and telomerase, isochores and gene distribution, "junk DNA"

Reading: Chapter 7

 

Sept. 17  no class

 

Sept. 21  Basic chromatin (JEH)

The nucleosome, higher order structures, MNase and DNaseI protection,

acetylation, methylation, phosphorylation of histones

Reading:  Chapter 7

 

Sept. 24  Gene silencing (JEH)

Sir2 and the assembly of inactive chromatin.  Telomere position effects and position effect variegation,   Clr4/Swit6 assembly of heterochromatin. 

Reading:  p. 556 ff. 

 

Sept. 28   X chromosome inactivation and imprinting. (JEH)

Reading: 

 

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

Reading:  Chapter 8

 

Oct. 12  DNA replication 3   (JEH)

S phase and cell cycle regulation; licensing

Reading:  Chapter 8

 

Oct. 15  DNA repair and recombination   (JEH)

Replication restart and recombination, break-induced replication and gene conversion

Reading:  Chapter 10

 

Oct. 19  DNA repair (JEH)

Mismatch repair, NER, bypass polymerases

Reading:  Chapter 9

 

Oct. 22   Transcription 1   (SK)

Polymerases, promoter structure, initiation site, PIC formation, holoenzyme

Reading:  Chapter 12

 

Oct. 29  Transcription 2 (SK)

TAFs, mechanisms of TAFs, upstream activators, enhancers, mediators, insulators

Reading:  Chapter 16-17

 

Nov. 2  Transcription 3 (SK)

Relationship to chromatin modification – insulators etc.

Reading: Chapter 16-17

 

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

Reading: Chapter 13 (until last section)

 

Nov. 16  Splicing 2   (SK)

Alternative splicing, polyadenylation, RNA editing

Reading: Chapter 13 (Last Section)

 

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)

Reading: Chapter 14-15

 

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) 

Reading:  Sections 11.3 and 11.4

 

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.