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How did we find out what a gene is?

The word "gene" originally meant a piece of DNA in chromosomes that controlled a given bodily trait. 

Basic plan for DNA: information is carried in the ordering of two pairs of molecules, adenine-thymine (A-T) and cytosine-guanine (C-G). Billions of such pairs line up in a specific sequence. When a cell divides, the DNA splits, where the dashed lines are in the diagram. Because C can only react with G and A only with T, the new cell creates an identical copy of DNA.
Diagram of DNA Plan

This scheme was discovered in a famous analysis of data that other people were generating at the time by Francis Crick and James Watson. The most useful data came from x-ray crystallography, which captures on film the x-ray scattering produced by crystals of DNA. The patterns, plus what others had learned about A, T, C, and G, led them to conclude the these molecules occurred in pairs and that the pair was held together by a weak bonds involving hydrogen. Each pair is called a "base pair," and the entire sequence of base pairs is called the "genome." So now, the question is:

If the genetic code is nothing more than the chain of A-Ts and C-Gs, how do we know what a gene is? That is, where does one segment (gene) end and another begin?

Discovery Base-Pair Sequences: Gene Mapping

  • First maps were done in fruit flies, because they have a small genome and because they have been used so often in genetic experiments
  • Now mostly complete maps exist for humans (about 3 billion base pairs).
But how do they know which base pair begins a gene and which ends a gene? The key is to know the sequence of base pairs that make a functioning protein. A combination of three approaches is used, and computers keep track of the information. Scientist Image
  • Certain short chains of base pairs are known to be markers for the beginning and ending of base-pair sequences that make a functioning protein.
  • A large series of enzymes exist that can cut DNA into smaller pieces. By splitting the two strands, one of the strands can be probed with a single strand from a known gene, for example a bacterial gene that makes a protein with a known function. The base sequence that matches the probe sequence is then identified as a gene
  • Insert an unknown piece of DNA into a bacterium or cell, and test for any new protein product that appears.

The results of such sequencing approaches led to the conclusion that the human may have only about 25,000 genes, which amount to only about 1% of the total genome. That is only about twice the number that fruit flies have. Does that make sense?  We are more than twice the animal a fruit fly is. How come we only have twice the genes? A few species have more genes that people do! Possible explanations include:

  • the proteins humans make are more complex than those usually made by fruit flies. 
  • humans have many more "regulatory genes," which are genes that turn on or turn off other genes.
  • many genes may work together to make a protein and each combination can make a different protein.

Humans apparently have a lot of genetic "junk." Huge fractions of our genome don't seem to do anything.  Some seem to be residues from viral and bacterial infections in our ancestors. So does this "junk" do anything? One obvious possibility is that it is a source of mutations.

It seems clear that our understanding is only just beginning. Even if we were sure what a gene is, we don't know what most of them do, nor what turns them on or off. We have only begun to consider the possibility that several genes are involved in making a single protein, as is the case with the workings of the body's immune system.


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