Dr. Gerald Johnson, LS 317 Office Hours: Tu/Th 5-6 PM [or by appt]

Office Phone 594-5371 Department of Biology - Message - 594-6442

e-mail gjohnson@sunstroke.sdsu.edu

TEXT: Benjamin Lewin, GENES VI, 1997

Chapter 5 Nucleic acid structure

Chapter 17 Topological manipulation of DNA [pp. 550-553]

Chapter 15 DNA replication

Chapter 16 Restriction and Repair [pp. 515-528 - Dealing with injuries in DNA]

Chapter 26 Chromosomes [pp. 763-767 - Telomeres]

Exam I FEB 26

Chapter 11 Transcription

Chapter 12 The operon [to p 365]

Chapter 28 Initiation of transcription

Exam II APR 2

Chapter 37 Oncogenes and cancer

Chapter 8 Protein synthesis [pp. 207-209]

Chapter 30 Nuclear splicing

Exam III MAY 12

PRELIMINARY SUBMISSION APRIL 30
FINAL SUBMISSION MAY 21

YOU SHOULD PROVIDE AN INDEPENDENT SUMMARY AND CRITIQUE OF THE ARTICLE

MONOALLELICALLY EXPRESSED GENE RELATED TO P53 AT 1P36, A REGION FREQUENTLY DELETED IN NEUROBLASTOMA AND OTHER HUMAN CANCERS. KAGHAD, BONNET, YANG, CREANCLER, BISCAN, VALENT, MINTY, CHALON, FERRARA, MCKEON AND CAPUT. [1997] CELL 90, 809-819.

AN INTRODUCTION/PERSPECTIVE TO THIS ARTICLE IS PROVIDED IN:

LONELY NO MORE: P53 FINDS ITS KIN IN A TUMOR SUPPRESSOR HAVEN. OREN [1997] CELL 90, 829-832.

INCLUDE THE FOLLOWING IN YOUR ANALYSIS AND CRITIQUE

I. BACKGROUND - A SUMMARY OF PRIOR OBSERVATIONS RELEVANT TO THE PAPER

II. RATIONALE - THE EXPERIMENTAL APPROACH UTILIZED IN THE PAPER, AND AN EXPLANATION OF HOW THIS APPROACH IS USED TO OBTAIN SIGNIFICANT NEW RESULTS

III. MATERIALS AND METHODS - A LISTING, WITH EXPLICATION, OF ALL METHODS AND MATERIALS USED TO OBTAIN ANY SIGNIFICANT RESULT IN THE PAPER

YOU NEED NOT LOOK UP INFORMATION IN PRIOR PUBLICATIONS NOR DESCRIBE IN FULL THOSE MATERIALS AND METHODS REFERRED TO IN PRIOR PUBLICATIONS

IV. RESULTS - AN EXPLANATION OF ALL IMPORTANT EXPERIMENTAL DETERMINATIONS

PRIMARY RESULTS WILL BE OBTAINED FROM THE FIGURES AND TABLES AND TEXT DISCUSSION

BE THOROUGH IN YOUR EXPLANATION OF RESULTS AND INCLUDE CONSIDERATION OF RELEVANT CONTROL DETERMINATIONS

V. DISCUSSION - A SUMMARY OF THE RELEVANCE OF THESE STUDIES TO FURTHER CHARACTERIZATION OF BIOLOGICAL PROCESSES

INCLUDE CONSIDERATION OF POINTS REMAINING UNKNOWN OR UNRESOLVED BY THESE STUDIES

IT IS ANTICIPATED THAT THE ANALYSIS/CRITIQUE SHOULD BE ACCOMPLISHED WITHIN A 5 PAGE MAXIMUM

WARNINGS -

YOU MUST PROVIDE AN INDEPENDENT CRITIQUE AND ANALYSIS

YOU MAY NEITHER COPY NOR PARAPHRASE THE ARTICLE

ASSIGNED PRIMARY LITERATURE FOR IN-CLASS DISCUSSION

DNA REPLICATION

Josse, Kaiser and Kornberg [1961] Enzymatic Synthesis of Deoxyribonucleic Acid

J Biol Chem 236, 864-875.

Brown and Cozzarelli [1979] A sign Inversion Mechanism for Enzymatic Supercoiling of DNA. Science 206, 1081-1083.

Baker, Sekimizu, Funnell and Kornberg [1986] Extensive Unwinding of the Plasmid Template during Staged Enzymatic Initiation of DNA Replication from the Origin of the Escherichia coli Chromosome. Cell, 45, 53-64.

Wu, Zechner and Marians [1992] Coordinated Leading- and Lagging-strand Synthesis at the Escherichia coli DNA Replication Fork. J Biol Chem 267, 4030-4035 [not entire article].

Muzyczka, Poland and Bessman [1972] Studies on the Biochemical Basis of Spontaneous Mutation. J Biol Chem 247, 7116-7122.

Wood, Robins and Lindahl [1988] Complementation of the Xeroderma Pigmentosum DNA Repair Defect in Cell-Free Extracts. Cell 53, 97-106

Kim et al [1994] Specific Association of Human Telomerase Activity with Immortal Cells and Cancer. Science 266, 2011-2015.

TRANSCRIPTION

Burgess, Travers, Dunn and Bautz [1969] Factor Stimulating Transcription by RNA Polymerase. Nature 221, 43-46.

Kassavetis and Geiduschek [1984] Defining a bacteriophage T4 late promoter: Bacteriophage T4 gene 55 suffices for directing late promoter recognition. PNAS 81, 5101-5105.

Schmitz and Galas [1979] The interaction of RNA polymerase and lac repressor with the lac control region. Nucleic Acids Research 6, 111-121 [not entire article].

Hochschild and Ptashne [1986] Cooperative Binding of Lambda Repressors to Sites Separated by Integral Turns of the DNA Helix. Cell 44, 681-687.

Oehler, Eismann, Kramer and Muller-Hill [1990] The three operators of the lac operon cooperate in repression. The EMBO Journal 9, 973-979.

Sakonju and Brown [1982] Contact Points between a Positive Transcription Factor and the Xenopus 5S RNA Gene. Cell 31, 395-405.

Bogenhagen, Wormington and Brown [1982] Stable Transcription Complexes of Xenopus 5S RNA Genes: A Means to Maintain the Differentiated State. Cell 28, 413- 421.

Braun, Riggs, Kassavetis and Geiduschek [1989] Multiple states of protein-DNA interaction in the assembly of transcription complexes on Saccharomyces cerevisiae 5S ribosomal RNA genes. PNAS 86, 2530-2534.

Banerji, Rusconi and Schaffner [1981] Expression of a beta-Globin Gene Is Enhanced by Remote SV40 DNA Sequences. Cell 27, 299-308.

ONCOGENES

Land, Parada and Weinberg [1983] Tumorigenic conversion of primary embryo fibroblasts requires at least two cooperating oncogenes. Nature 304, 596-601.

Finlay, Hinds and Levine [1989] The p53 Proto-Oncogene Can Act as a Suppressor of Transformation. Cell 57, 1083-1093.

Pietenpol, Tokino, Thiagalingam, El-Deiry, Kinzler and Vogelstein. [1994] Sequence- specific transcriptional activation is essential for growth suppression by p53. Proc. Natl. Acad. Sci. USA 91, 1998-2002.

RIBOSOMES

Noller, Hoffrath and Zimniak [1992] Unusual Resistance of Peptidyl Transferase to Protein Extraction Procedures. Science 256, 1416-1419.

RNA PROCESSING

Grabowski and Sharp [1986] Affinity Chromatography of Splicing Complexes: U2, U5, and U4+U6 Small Nuclear Ribonucleoprotein Particles in the Spliceosome. Science 233, 1294-1299.

Zhuang and Weiner [1986] A Compensatory Base Change in U1 snRNA Suppresses a 5' Splice Site Mutation. Cell 46, 827-831 [not entire article].

Inoue, Hoshijima, Sakamoto and Shimura [1990] Binding of the Drosophila Sex-lethal gene product to the alternative splice site of transformer primary transcript. Nature 344, 461-463.