Monday, March 22, 2010

The Basics of DNA and RNA:

What's DNA?
This gives us all the information on how to make our cells.  It's like a genetic blueprint, used to synthesize proteins and other molecules. 

What's RNA? 
RNA is the copy of the blueprint that goes to the building crew.  DNA isn't directly read to make proteins, so RNA is used as the copy.  The process of making an RNA copy of DNA is called transcription, and the process of making a protein from RNA is called translation.  The RNA uses a protein called a ribosome to actually manufacture the protein. So the DNA is the master design, the RNA is the blueprint copy,  and the ribosome is the work crew that assembles the protein.

What cats can teach us about our genes

Let's think of DNA and RNA molecules like they're sentences that will tell our building crew what to make.  So we're thinking of a string of words, made of letters.   Our example sentence will be: "Tag a cut cat".  The example letters in this sentence (T, A, G, U and C) are called nucleotides, which are 3-part structures that contain a pentose sugar and a nitrogenous base.  In real life, there are 5 nitrogeous bases (these are called "nucleosides") which are used for both DNA and RNA.  Their names are adenine, guanine, cytosine, uracil and thymine.  However, the pentose sugar is different in DNA than in RNA: in RNA we use ribose, and in DNA we use deoxyribose, which means that one oxygen atom has been replaced with a hydrogen.  When the sugar and the base are bound together, the resulting molecule is called a nucleotide - the letters that we mentioned earlier.  In real life, the name of the nucleoside gives the letters, so adenine = A, cytosine = C, Uracil = U, guanine = G and Thymine = T, which match the letters in our example.

So how do we connect the letters (the nucleotides) to make words?  This is done by using a high energy phosphate bond, which attaches to the 3 and 5 carbon position of the sugar molecules.  These link the nucleosides into a chain, and because each phosphate is linked to two sugars, the connection is called a phosphodiester bond.  What's so special about this kind of linkage?

The nucleotide cowboy dance
The key feature of a phosphate group is the number of oxygens it contains.  Oxygen is very electronegative: it acts like an electron vacuum, pulling the electrons away from the interior phosphorous.  So anything bound to it often has an induced negative charge, because it's partner loses some electron density to oxygen.  But there's an even stronger effect when it's specifically bound to phosphorous, because this atom needs to make 5 bonds, but only uses 4 oxygen atoms to make the connection.  So the phosphate group (the phosphorous and oxygen) has an overall negative charge.  This makes it happy to associate with water, which also carries a slight charge.

 At the same time, the nucleotides aren't carrying a charge, and they're not so happy to associate with anything that is charged.  So the nucleotides want to aggregate together, and the phosphate groups want to associate with themselves or water.  This is what makes DNA have it's double helical nature:  the connection between the nucleotides and the phosphates restricts how the entire structure can bend or twist.  So having the nucleotides face each other, with the phosphates on the outside, protects the nucleotides from water without limiting the phosphate's ability to make the same interactions.  You can think of the nucleotides like an old fashioned line dance, with the partners facing each other, but holding hands with their left and right hand neighbors.

So now we have our nucleotides linked together, and we have them in the configuration they like best. Our blueprint is nice and tidy, but what do we do now?   How do we actually read the words in our DNA?  How do we even know what those words are? We'll talk about that in the next post.


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