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Project Summary
| Difficulty | 10 |
| Time required | Long (a couple of weeks) to Very Long (several weeks to months) |
| Prerequisites | Advanced biology course, or willingness to read up on such topics extensively. |
| Material Availability | A computer with Internet access is necessary for this project. |
| Cost | Very Low (under $20) |
| Safety | No issues |
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Sponsor
| Sponsored by generous grants from Bio-Rad and its Biotechnology Explorer program |
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| Inspiring minds want to know. Unravel the mysteries of biotech |
| explorer.bio-rad.com |
| * Note: This is an abbreviated project idea, without notes to start your background research or a procedure for how to do the experiment. You can identify abbreviated project ideas by the asterisk at the end of the title. If you want a project idea with full instructions, please pick one without an asterisk. |
Abstract
Some sequences of RNA can catalyze biochemical reactions, much like protein enzymes. These catalytic RNA sequences are called ribozymes. The function of a ribozyme depends upon the primary sequence of the RNA which folds into a 3-D structure. How do different ribozyme sequences fold? You can search for ribozyme sequences using Entrez BLAST (NCBI, 2006). Then you can use a program like MFOLD (http://bioweb.pasteur.fr/seqanal/interfaces/mfold-simple.html) to submit your sequence for an analysis of its predicted 3-D structures based upon thermodynamics (Zuker, 2006; Zuker, 2003). Compare the different predicted structures and see if they are similar or different. If possible, compare the predicted structures to a published crystal structure. How close was the predicted structure to the crystal structure? Can you identify primary sequence elements in your molecule that contribute to parts of the structure? For example, palindromic stretches can form stem-loop structures. You can also mutate the sequence and submit the new sequence to MFOLD. How does this alter the 3-D structure? Can you use this computational method to identify potentially important nucleotides?Bibliography
National Center for Biotechnology Information. (2006). Entrez PubMed. Retrieved March 25, 2006, from http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db.Variations
- For more science project ideas in this area of science, see Biotechnology Project Ideas.
Last edit date: 2008-11-10 15:10:22
Career Focus
If you like this project, you might want to think about career opportunities in
Biotechnology.
Growing, aging, digesting—all of these are examples of chemical processes performed by living organisms. Biochemists study how these types of chemical actions happen in cells and tissues, and monitor what effects new substances, like food additives and medicines, have on living organisms. Learn more about this career: Biochemist.
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