The Genome - Going from Letters to Words, Part 1

Let's start with a quick review of our earlier discussions on DNA/RNA.   We said that DNA is our master blueprint, and RNA is like a copy of those instructions that goes to the builders.  We briefly distinguished DNA from RNA by how their sugars are different:  DNA uses deoxyribose and RNA uses ribose. We also said that nucleotides are used to make both molecules, and we discussed how in both cases, the nucleotides are arranged in linear strands, like beads on a string.  We compared the DNA structure to a set of line dancers: one line holding hands with the left and right dancers, and standing opposite their partners.  In DNA there are connections between the two strands, which cause the winding and characteristic double helix form.

This is a picture like the last one we saw.  We can see that the A (adenine) always pairs to T (thymine) and the G (guanine) to C (cytosine).  It's like our line dancers are forced to always choose certain partners to dance with.  In DNA, this forced interaction is because of the bonding between facing pairs: these are the light dashes between the nucleotides.  These are hydrogen bonds between the electronegative (electron withdrawing) nitrogens and oxygens, and the hydrogens on their faced partners.  This is a much weaker kind of bonding than what happens between the side-by-side neighbors (about 1/10th the strength) but these bonds are strong enough to stabilize the structure.  Anytime a structure, how it's bent/shaped or it's position to another object is stabilized, it costs energy to have it not be that way. It's like taking the pacifier away from the baby -- there's a price to pay.  In general, Nature spends energy reluctantly: lower energy means something is more likely to occur. 

So now we have our dancers in two lines facing each other, like a bunch of middle-schoolers in 6th period gym.  For the sake of this example, the kids are named after each nucleotide (so we've got a room of kids, but just 4 names among them.)  Their teacher, Mr. Chargaff, puts them in Group 1 and Group 2, and tells each group to stand in line.  Then he tells them they have to pick partners from the opposite group, and the same partners each time.   What does he tell the substitute teacher to worry about?  What can she gloss over?

The Influence of Primary Structure
Chargraff's rules tell us that all we need to worry about is lining up one line of kids. Once we have that figured out, the position of the other children is automatically enforced.   So if the Group 1 kids are lined up as:

A, T, C, C, G, A; then their partners will line themselves up as
T, A, G, G, C, T, and vice versa.

If the Group 1 kids line up as C, T, C, C, A, A;
then their partners line up as  G, A, G, G, T,  T.

So we only need to get one group of kids organized, and the other kids do the work for us.  The genetic code works in a similar fashion: once we know the line up of one strand, the second strand is precisely defined.  RNA exploits this effect -- it's generally single stranded, which is all that's needed to make an accurate copy of the DNA master print.

So we have a line up of nucleotides.  Where does that get us?

How Robots are like Hamburgers

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

DNA and RNA

This week, we'll be taking a diversion and discussing how genes work. So the topics will include the basics of gene transcription, translation and splicing. There's some interesting work on gene therapies and so we'll develop the vocabulary to discuss these issues.