Schedule and Readings for Schleif's Portion of Graduate Biophysical Chemistry, 2018
The following papers are available online through the Hopkins lilbrary. The book chapters are from "Genetics and Molecular Biology" by R. Schleif. You can download the
pdf of the entire book from this link.
1 Cell Structure, Feb. 15, Chap. 1
Inside a Living Cell, Goodsell, D., Trends in Biochemical
Sciences 16, 203-206 (1991).
2 Nucleic Acid Structure, Feb. 20, Chap. 2
DNA Flexibility Studied by Covalent Closure of Short
Fragments into Circles, D. Shore, J. Langoushi, R. Baldwin,
Proc. Natl. Acad. Sci. USA 78, 4833-4837 (1981).
3 DNA Synthesis, Feb.22, Chap. 3
E. coli oriC and
the dnaAGene Promoters are Sequestered from dam
Methyltransferase Following the Passage of the Chromosomal
Replication Fork, Campbell, J., Kleckner, N., Cell 62,
967-979 (1990).
4 RNA Synthesis, Feb. 27, Chap. 4
Transcription Against an Applied Force, H. Yin, M. Wang, K.
Svoboda, R. Landick, S. Block, J. Gelles, Science 270,
1653-1657 (1995).
5 RNA Synthesis Mar.1
Promoter unwinding and promoter clearance by RNA polymerase:
Detection by single-molecule DNA nanomanipulation Andrey
Revyakin, Richard H. Ebright, and Terence R. Strick, Proc.
Nat. Acad. Sci. USA 101, 4778-80 (2004).
6 Protein Structure Mar. 29, Chap. 6
Rapidly scan
Macromolecular Modeling with Rosetta, R. Das, D. Baker, Annual Rev. Biochem,
77, 363-382 (2008).
Study the material at https://gremlin2.bakerlab.org/index.php
Rapidly scan
Protein Structure Determination using Metagenome Sequence Data. S.
Ovchinnikov, H. Park, N.Varghese, P. Huang, G. Pavlopoulos, D.
Kim, H. Kamisetty, N. Kyrpides, D. Baker. Science, 355 294-298, (2017).
Global Analysis of Protein Folding Using Massively Parallel Design,
Synthesis and Testing, G. Rocklin, T. Chidyausiku, I. Goreshnik, A.
Ford, S. Houliston, A. Lemak, L. Carter, R. Ravichandran, V.
Mulligan, A. Chevalier, C. Arrowsmith, D. Baker. Science. 357, 168-175 (2017).
7 Protein Synthesis April 3, Chap. 7
Expanded Genetic Code, Wikipedia
https://en.wikipedia.org/wiki/Expanded_genetic_code
Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA,
K. Keiler, P. Waller, R. Sauer, Science 271, 990-993.
8 Gene Regulation April 5, If you don't know the standard stuff on the lac operon, read Chap.11
AraC Protein, Regulation of the L-arabinose Operon in Escherichia coli, and the Light Switch Mechanism of AraC Action, FEMS Microbiology Reviews 34, 779-798 (2010).
9 Genetics and Probability Distributions April 10,