03/20/2003
Expressions. Part 1
Next year will mark the 60th anniversary of the publication in 1944 of a little book by Erwin Schrodinger (umlaut over the “o”) titled “What is Life?” Schrodinger, whose wave equation is the basic equation of quantum mechanics, speculated that the genetic stuff in our cells contained some kind of code that could explain life’s diversity and its perpetuation. That same year, Oswald Avery and his colleagues Collin MacLeod and Maclyn McCarthy published the results of their work on smooth-surfaced and rough-surfaced bacteria. They managed to extract some material from the smooth-surfaced bacteria and introduce it into rough- surfaced bacteria. The latter transformed into the former! They found the material to be DNA. This year, 2003, marks the 50th anniversary of Watson and Crick’s discovery of the DNA double helix as the master code of life that Schrodinger postulated.
The media have celebrated this 50th anniversary with many articles and programs on Watson and Crick and the fascinating events leading to their breakthrough discovery. Brian Trumbore called my attention to two of these articles in the February 24/March 3 issue of U. S. News & World Report – “Triumph of the Helix” by Nell Boyce and “DNA meets its Match” by Thomas Hayden. The latter article deals with the increasing attention being paid to RNA, the guy who takes the instructions from DNA and scurries over to the chemical factory in the cell and tells it what protein to manufacture. In this dynamic duo of DNA and RNA, RNA has been sort of the Rodney Dangerfield of the two, its messenger boy status gaining it little respect compared to the attention accorded DNA. This situation has changed drastically and “small” RNAs were named the “Breakthrough of the Year” in last year’s December 20 issue of Science.
It turns out that RNA in its various forms is much more than just a messenger. Indeed, current thinking is that RNA is not a cousin to DNA but probably was its ancestor. Recent findings show that a small RNA enzyme can build up other forms of RNA, suggesting that RNA could once duplicate itself. Today, workers are turning up evidence that RNA plays key roles in controlling what goes on in a cell as, for example, in “gene expression”. What is gene expression? For that matter, what is a gene? Obviously, the definition of a gene isn’t all that clear-cut or we wouldn’t have found that our own recently decoded human genome actually contains several tens of thousands fewer genes than most researchers expected! The definitions of a gene that I find boil down to something like this: a gene is a unit by which traits are passed from one generation to another. Chemically, a gene is a length of DNA that codes for a particular protein or peptide. What are proteins and peptides?
Wait a minute. I’ve often said that my mind glazes over when I confront these complex biochemical subjects. It’s high time that I knuckle down and make a serious effort to understand some of this stuff. I’m warning you – it may be rough going and it might take a couple of columns before I’m either satisfied or fed up! Let’s start from the bottom and work our way up to the complex stuff. First, a basic unit is the amino acid – an organic compound that has both a COOH and at least one NH2 group in its formula. The COOH is the acid part and the nitrogen-containing NH2 group is the amino part. Why are amino acids important to us? They can react to form peptides, which are “simply” some amino acids linked together through interactions between adjacent COOH and NH2 groups. Now suppose we hook a bunch of peptides together – we have a polypeptide.
Who cares about polypeptides? We all should care. Chain a bunch of polypeptides together and you have a protein. A protein can have hundreds or thousands of amino acid groups in it. It was no small achievement when someone first determined the composition of a protein. Without proteins such as hemoglobin, antibodies, keratin and collagen (skin and bones), various enzymes, muscle proteins like actin and myosin, to name just a few, we wouldn’t be here. Proteins are the stuff of life in that respect.
With proteins more or less in hand, we can talk about “gene expression”. Gene expression is the process in the cell whereby a gene “expresses” itself, reveals its code, to the messenger RNA (mRNA), which then sees to it that the “factory” in the cell assembles the proper protein encoded in the gene. Simplistically, the RNA transcribes the code from the gene, goes to the factory, known as a ribosome, and tells the ribosome what amino acids to put together to make the coded protein. Actually, it’s much more complicated and we have to consider enzymes and “transfer RNA” (tRNA), which carries the amino acids up to the ribosome. This is still too simplistic, as I found when I read about the work of Dr. Danny Reinberg in an article by Eric Lerner in the Fall/Winter 2002 issue of Robert Wood Johnson Medicine. The article is titled “On the Trail of Gene Expression: The Mechanism That Shapes Different Cells”.
Reinberg and many others have been pursuing the answer to a very profound question. Why does a particular gene get transcribed (expressed) when it does and what controls this process? Every cell in our body has the same set of genes. Yet, a heart cell produces certain proteins at certain time while a skin cell produces and needs certain other proteins at different times. With each of our cells containing the same 30,000 or so genes, how do the heart cell and the skin cell know which genes should be expressed and which ones should stay “silent”? Before even attempting to answer these questions, let’s go back to basics again.
First, let’s talk nucleic acids. It was way back in 1869 when a Swiss fellow, Johann Friedrich Miescher, isolated “nucleic acid” from pus (ugh!). The basic unit here is the nucleotide, a complex chemical group that contains a nitrogen base linked to a sugar and a phosphate group. Nucleotides occur naturally and are quite important in the scheme of things, to put it mildly. One very important nucleotide is ATP (adenosine triphosphate), the energy source that powers the reactions going on inside our cells. String a bunch of nucleotides together in a polymer and you’ve got a nucleic acid.
Why be concerned with nucleic acids? Well, there are two types of nucleic acids that we know quite well – desoxyribonucleic acid, better known as DNA, and ribonucleic acid, RNA. The two compounds differ in the types of sugar groups they contain (desoxyribose and ribose, respectively) and one of the bases is different in RNA. The bases are the glamorous components of DNA, the famed A, C, G and T “letters” (adenine, cytosine, guanine and thymine) that form the genetic code. (RNA substitutes uracil for thymine.)
In DNA, A only bonds to T and C only bonds to G. This A-T, C- G pairing is the key to coding and perpetuation of the species. In the double helix structure, the two entwined six and a half foot long ribbons of DNA are linked by these A-T and C-G bonds. When a cell divides and the DNA ribbons disentwine to go their own ways, the A-T and C-G unique bonds are remanufactured and the resulting DNAs in the two cells are exact copies of the DNA in the parent cell. Once in a while, of course, there will be some “mistakes” and these mutations will either die out or flourish in succeeding generations.
So far, I’ve implied that the messenger RNA transcribes the gene’s DNA code by just running up and down the DNA and somehow copying the A-C-T-G code. It’s not that simple. The DNA isn’t just sitting there naked in the nucleus waiting for the RNA to unzip the double helix to read the code. Actually, the DNA is wrapped around spools of “histone” proteins. These spools are called nucleosomes. The DNA wrapped around the nucleosomes forms a fiber, only 11 nanometers across, that is called chromatin. In turn, the chromatin is coiled into a 30- nanometer fiber that is structured into more complex forms that eventually scale up to the chromosome that we know and love.
As if things aren’t complicated enough, RNA doesn’t read the DNA’s code directly. That is done by something call RNA polymerase II, which is the real workhorse that runs along the gene’s DNA and produces the messenger RNA. But to get the DNA to open up enough for it to squeeze in and read the right gene, the polymerase has to accomplish a couple of things. First, it has to find the start of the gene and “dock” there to begin its transcribing. To do this, it needs the assistance of so-called “growth transcription factors” (GTFs). There are at least six GTF molecules that have been identified to date. Four of these are involved in this docking process while the other two GTFs serve as “pushers” to prod the polymerase along its way down the DNA once it gets docked.
How does one gene become active and express itself while the other genes remain silent? It depends on how tightly the DNA is wrapped around the spools of histones. In a tightly wound section of chromatin, the GTFs and polymerase can’t get in and the gene is silent. In the loosely wound region, the GTFs and polymerase have room to do their transcribing job. That gene is expressed and the protein will be manufactured. OK, how do some sections of chromatin become tightly wound while others are loose?
I don’t know about you, but this effort to understand just a bit of what goes on in a minute single cell in our bodies has been quite exhausting. If I can gather sufficient energy, I will try to delve further into the gene expression next week and answer the question posed in the above paragraph. Putting the question in a different way – how does a heart cell know it’s a heart cell?
Allen F. Bortrum
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