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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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-03/20/2003-      
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Dr. Bortrum

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