-- %TEACHINGWEB%.TaiNg - 13 Oct 2011

HomeWorkFourPartOne

For YESdotoff. pdf, I don't know how to label the stem. But look at YESdoton.pdf and STEM I and III is conserved. But IV is longer and apparent

For Yesdoton.pdf, The STEM IV disappears but stem II now appears (shorter)

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For Homework part 2 see attachment rna.odt

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For Homework part III, look at attached Hammerhead structure. It is very different from the literature from * Wikipedia:Hammerhead_ribozyme mainly because the conditions at which the proteins fold were different. for example, we learned that during lab temperature plays a huge role in deciding how RNA fold. Also, the algorithm at which RNAfold and the program that Rfam used in determining the minimum free energy may be different. RNAfold and the Rfam version may have different setting parameters such as pH and also relative hydrophobicity of the environment (which may alter the way the nucleotide base pairs because both involves hydrogen bonding)