Lecture 3. Tuesday, September 5. Nucleic Acid Structure. Peptide conformations.

Lecture 3. Tuesday, September 5. Nucleic Acid Structure. Peptide conformations.

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Restricted: For students enrolled in CHEM 130/MCB 100A, UC Berkeley, Fall 2006 ONLY 1 John Kuriyan: University of California, Berkeley CHEM 130/MCB 100A. Lecture 3. Fall 2006. The standard (“Watson-Crick”) structure of DNA is called B- form: The grooves are defined by the positioning of the DNA base pairs with respect to the glycosidic bond:
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Restricted: For students enrolled in CHEM 130/MCB 100A, UC Berkeley, Fall 2006 ONLY 2 Top view of base pairing B-form DNA: The major and minor grooves of DNA differ in their hydrogen bonding capabilities:
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Restricted: For students enrolled in CHEM 130/MCB 100A, UC Berkeley, Fall 2006 ONLY 3 Conclusion: Major groove is more distinctive than minor groove. Transcription factors and other DNA-binding proteins with sequence specificity (e.g., restriction endonucleases, which cut DNA at sites defined precisely by a sequence) “read out” the sequence in the major groove. For example, the restriction endonuclease Eco RI cuts DNA at precisely this sequence: _____________________GAATTC___________________ _____________________CTTAAG___________________ In the major groove, this looks like this:
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Restricted: For students enrolled in CHEM 130/MCB 100A, UC Berkeley, Fall 2006 ONLY 4 While B-DNA is the most stable conformation for DNA, RNA cannot adopt this conformation. The reason has to do with sugar pucker: Usually the atom that is non-coplanar is the C2 or the C3 carbon: The 5 atoms in the sugar ring cannot be coplanar. One of the atoms pops out of the
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Lecture 3. Tuesday, September 5. Nucleic Acid Structure. Peptide conformations.

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