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MBB 222 Study Guide - Final Guide: Leucine Zipper, Structural Motif, Electronegativity

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School
Simon Fraser University
Department
Molec Biol & Biochem
Course
MBB 222
Professor
Edgar Young

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Document Summary

Mbb222 exam vocab definitions: transcription factor interfaces, combinatorial. Control, e. coli dna replication fork and replisome (dna polymerase domain) An independently folded protein domain that contains at least one structural motif that can recognize double or single stranded dna. To bind specifically to dna sequences, regulatory proteins must recognizes surface features on the dna. Most specificity is due to the recognition of hydrogen bonds (h-bond donor and acceptor groups) Major groove has more specificity than minor groove because more chemical information is present on major groove. An alpha-helix for binding with dna at a major groove. Functional groups in the major and minor groove of dna. Includes: h-bond acceptor, h-bond donor, other h and methyl group. Major groove has more chemical information (4 groups vs. 3 on minor groove) An acceptor is an electronegative atom with no h attached. A donor is an electronegative atom with an h attached.

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Related Questions

2. "Mycobacterium tuberculosis PhoP of the PhoP-PhoR two-component signaling system orchestrates a complex transcription program and is essential for the growth and virulence of the tubercle bacillus. PhoP comprises a phosphorylation domain at the amino-terminal half and a DNA-binding domain in the carboxy-terminal half of the protein. We show here that the protein recognizes a 23-bp sequence of the phoP upstream region comprising two adjacent direct repeat motifs believed to promote transcription regulation.
--Gupta et al. (2009) J Bacteriol. 191(24):7466-7476.
a. The helix-turn-helix motif allows for DNA binding in which groove of DNA?
b. Why does the major groove of DNA allow for more sequence-specific binding than does the minor groove?
c. The authors reported that proteins similar to PhoP form were thought to form head-to-head dimers. The dimerization would prevent it from interacting with the major groove of DNA. If the dimer could only bind the minor groove of DNA, how would that affect the specificity of DNA sequence-specific binding?
d. The authors found that with PhoP, the monomers find bind DNA and then the dimerization occurs. Why would that be necessary for proper sequence-specific recognition?