motif 332.mot.003 Louis J. Sheehan, Esquire

Bacteria have a different mechanism. When an incorrect/damaged mRNA is being translated, it “stalls” during the translation process and is not released. A special RNA – referred to as tmRNA – enters the ribosomal A-site and, upon its translation, the stalled mRNA and the ribosome are decoupled and the stalled (broken) mRNA is degraded.
Slides: T-14, T-15

5. Write about the following: cell differentiation; external signals and their effect on gene expression; DNA helix outside structure and its significance in recognition by DNA binding proteins.

(a) Cell differentiation: Generally, without altering their DNA sequence, cells in multicellular organisms differentiate as they synthesize different types of proein and RNA molecules.
Slide G-2
(b) External signals and their effect on gene expression: Multicelular organisms’ specialized cells can often alter their genetic expression vis-à-vis external cues. Different cell types can alter their expressions differently in the presence of the same external cue.
Slides G-4, G-5, G-6,G-7

(c) DNA helix outside structure and its significance in recognition by DNA binding proteins: The outside of the DNA double-helix is peppered with information recognized by gene regulatory proteins. Base-pair edges are exposed at the double-helix surface resulting in distinctive patterns in both the major and minor grooves of hydrogen bond donors, hydrogen bond acceptors, and hydrophobic patches. However, the patterns in the major grooves are more distinctive and, as such, gene regulatory proteins are more likely to make contact in the major grooves.
Slides G-12, G-13, G-14, G-15, G-16, G-17

6. Write about the following: Helix-turn-helix Motif, zinc finger motif, beta sheet proteins, helix-loop-helix motif; heterodimerization.

(a) Helix-turn-helix motif: This is a DNA binding protein motif. It is a “turn” comprised of two alpha-helices connected by a short extended chain of amino acids. Interactions between the two helices hold the two helices at a fixed angles. Because it fits into the major groove, the C-terminal helix is called the “recognition helix”; amino acid side-chains are involved in recognizing the specific DNA sequence to which the proteins bind. Note, however, that the structure of the various proteins that contain this motif vary, and, therefore, each protein presents this motif to DNA in a different way (this increases the number of DNA sequences that the motif can be used to recognize). Additionally, parts of the polypeptide chains outside the helix-turn-helix domain engender contacts with the DNA, providing even more specificity.
(b) Zinc finger motif: This DNA binding protein motif includes zinc as a structural element. There are many types of zinc finger motifs.
(c) Beta sheet protein: Here a two-stranded beta sheet with amino acid side chains extending toward the DNA reads the information on the major groove. The exact DNA sequence recognized depends upon the amino acids that make up the Beta sheet(s).
(d) Helix-loop-helix motif: This motif consists of a short alpha helix connected by a loop to a longer second helix. The two alpha helices that extend from the dimerization interface connect with the DNA.
(e) Heterodimerization: Some helix-loop-helix proteins lack the binding alpha extensions and thus have only half the number of DNA contacts.; this is yet another way to hold specific gene regulatory proteins in check.
Slides G-11, G-18, G-19, G-20, G-21, G-22, G-23, G-24, G-25, G-26