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16S rRNA gene
What is the 16S rRNA Gene?  
    The 16S rRNA gene is a section of prokaryotic DNA found in all bacteria and archaea.  This gene codes for an rRNA, and this rRNA in turn makes up part of the ribosome.  The first 'r' in rRNA stands for ribosomal.  The ribosome is composed of two subunits, the large subunit (LSU) and the small subunit (SSU).  These two subunits sandwich the mRNA as it feeds through the ribosome for translation.  While there are also associated proteins helping to make up the functional units of the ribosome, in general, in bacteria, the SSU is coded for by the the 16S rRNA gene, and the LSU is coded for by the 23S rRNA & 5S rRNA genes.
Why is it Used?    
    The 16S rRNA gene is a commonly used tool for identifying bacteria for several reasons.  First, traditional characterization depended upon phenotypic traits like gram positive or gram negative, bacillus or coccus, etc. Taxonomists today consider analysis of an organism's DNA more reliable than classification based solely on phenotypes. Secondly,
researchers may, for a number of reasons, want to identify or classify only the bacteria within a given environmental or medical sample.  While there is a homologous gene in eukaryotes, the 18S rRNA gene, it is distinct, thereby rendering the 16S rRNA gene a useful tool for extracting and identifying bacteria as separate from plant, animal, fungal, and protist DNA within the same sample.  Thirdly, the 16S rRNA gene is relatively short at 1.5 kb, making it faster and cheaper to sequence than many other unique bacterial genes.  
How
is it Used?   
Ribosomes (and correspondingly the DNA that codes for them) have been mostly conserved over time, meaning that their structure has changed very little over time due to their important function, translating mRNA into proteins. But even within this gene there are parts that have been conserved more than others.  This is due to the structure of the ribosome itself.  With the way the ribosome folds, creating bonds with itself in some places (conserved regions) while other portions are looped and unbonded (hypervariable regions), the degree to which any portion of the gene is subject to mutations varies.



SSU & LSU portions of RibosomeGrThre

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