Biology concepts – DNA, RNA, tRNA, nonstandard nucleotides, codon,
anticodon, genetic code, selenocysteine, isodecoder, mitochondria
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Just
looking the Imperial Hotel in Tokyo doesn’t really give us an idea
of
why they inspired Frank Lloyd Wright’s son to invent Lincoln Logs.
It was the interlocking beams of the
basement in which his vision was
born.
They were supposed to protect the hotel from earthquake
damage.
It worked. In 1923, the same year the hotel was finished,
there
was a great earthquake in Tokyo and the Imperial was one of
the
few buildings that survived. It also survived the bombings of
WWII. So they tore it down in 1968.
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The first edition of Lincoln Logs, sold in 1918, gave
instructions for building Abraham Lincoln’s boyhood home and Uncle Tom’s cabin.
The parts were commensurate for building those structures. Each set of
instructions called for the small pieces to be put together in a certain order so
that the resulting product conferred a meaning – this is where Lincoln grew up
or this is where Tom lived.
DNA and RNA are similarly constructed. There are a few
pieces (nucleotides A, C, G, T, and U) that can be used to build different
structures. Each small piece can be joined with other small pieces to become part
of the whole structure, a structure with meaning. In the case of DNA and mRNA,
three nucleotides in a row can confer meaning for one protein building block.
The entire series of nucleotides then has the meaning of an entire protein.
The three nucleotide codons relate
to a certain amino acid building block to be inserted into a growing protein.
This code, the genetic code, gives
meaning to the string of DNA nucleotides in genes and the string of nucleotides
in the mRNA transcribed from the gene. This is usually where our learning about nucleic acids ends.
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The
top left picture is Marshall Nirenberg, the initial decoder of the
genetic
code. The right photo is Robert Holley, discoverer of tRNA.
Below
is the genetic code in graphic style. The four large letters
represent
the possible first bases of a codon (in mRNA). The light
yellow
letters are the possible 2nd bases, and the darker yellow letters
are
the final possibilities. Outside are the amino acids that are coded
by
the individual codons. Note that most have more than one codon
and
some have codons that begins with different letters, like serine
at 1:00 and 8:30.
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But I digress – let’s talk briefly how we decoded the pathway of
gene to protein. It begins with Watson and Crick publishing the structure of
DNA in 1953. We knew how the different bases could be ordered, but we still
didn’t know how they called for a specific amino acid sequence.
In 1955, Francis Crick thought he had an idea about how it
might occur, but he didn’t have all the players. He called his idea the Adapter Hypothesis. What he was missing
was the adapter, the piece that he said carried amino acids and put them in the
correct order.
One neat trick came from George Gamow, a nuclear physicist
best known for his role in theorizing the Big Bang (the birth of elements from
a cosmic explosion, not the TV show). We had four nucleotides to encode
information and 20 (you and I know there are 22) amino acids to be coded for.
He used some “way beyond me” math to determine that the most efficient
mechanism would have three nucleotides code for one amino acid.
This was followed by an interesting experiment done by
Marshall Nirenberg at the National Institutes of Health near Washington, DC. He
made a synthetic RNA of a single nucleotide (UUUUU….). He then combined this
with the innards of a bunch of cells (cell lysate) so that everything needed to
make a protein would be present. He detected a peptide of phenylalanine amino
acids. What is more, there were 1/3 as many amino acids as there were
nucleotides!
So UUU coded for phenylalanine. This was followed by many
more experiments using different sequences of nucleotides, and the code was
decoded. Along with this knowledge came the discovery of tRNA by Robert Holley in 1965. This RNA combined an anticodon sequence to recognize a codon
on mRNA and carried the appropriate
amino acid at the other end. The tRNA was Crick’s adapter, and perhaps the code
would have discovered years earlier if the adapter had been pursued in earnest.
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The
process of turning an mRNA into a protein involves the ribosome and
the
tRNAs. When an mRNA is bound to a ribosome, the three nucleotides
in
the codon (pink letters) match with three letters of a tRNA anticodon
(blue
letters). Different tRNAs will drift in and out until the right one is
bound.
The tRNA has the amino acid (aa) bound to the end opposite the
anticodon.
If this is the first position of the peptide, it will occur in the P
(peptidyl)
site. The second tRNA will be added to the A (acceptor) site and
the
ribosome will shift as it creates a peptide bond between the two aa’s.
The
shift puts the first aa in the E (exit) site to reelase the tRNA, the 2nd
aa
goes to the P site, and the A site is open for the next tRNA.
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In most cases, codons that call for the same amino acid have
the same first two nucleotides; it’s the third position (wobble position) that varies. It was
discovered that the third position of the anticodon binds to the DNA very
loosely, so the codon/anticodon binding is usually determined by the first two
nucleotides. This allows a single tRNA to recognize more than one codon.
It turns out that there are 40-55 different tRNAs, depending
on the organism. Why so many? As an example, arginine is coded for by several
codons (CGG, CGA, CGC, CGU, AAC, and AAU). It is impossible for one tRNA to
recognize both AAC and CGG, so there must be more than one tRNA for arginine.
Serine and leucine are like this as well, and there are most
certainly some amino acids whose tRNAs can’t bind to all four possible
nucleotides in the wobble position (like glycine), so they would need more than
one tRNA. These are the isodecoder tRNAs
(different anticodons, but code for same amino acid).
There are also different isodecoder tRNA genes, having
different sequences outside the
anticodon, but code for the same amino acid. Humans have about 274 genes for
our 55 different tRNAs. This implies that the different sequences might have
some functions other than just
helping to add the right amino acid to a growing peptide sequence.
A 2010 minireview talked about those possible tRNA functions.
In one discussed study, a cleaved tRNA is shown to have increased expression when
cells are proliferating. Reducing the levels of this cleavage product reduced
the rate of cell division. In another study, a tRNA cleavage product silenced
the expression of a specific gene. I’ve said it before: nature abhors a
unitasker.
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UGA,
UAA, and UAG are the most common stop codons (see the text for the
exceptions).
When the stop codon ends up in the A site, no tRNA fits properly,
but
a releasing factor (RF) can be bound. There are at least two RF, RF-1
recognizes
UAA and UAG; RF-2 recognizes UAA and UGA. When bound they
cause the ribosome to fall apart.
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There are also three codons that don’t code for an amino
acid. These are the stop codons that tell the ribosome to stop making the
protein and release it.
So we have coding codons and noncoding codons. Experiments in other organisms in the 1960’s and 1970’s indicated that all life uses the same genetic code, making it the universal genetic code. And here begins the exceptions.
So we have coding codons and noncoding codons. Experiments in other organisms in the 1960’s and 1970’s indicated that all life uses the same genetic code, making it the universal genetic code. And here begins the exceptions.
The genetic code is almost
universal. Considering how many genes from how many organisms there are, the
number of exceptions is relatively low. But they are still too numerous for us
to talk about them all. That doesn’t mean we should talk about a few of the
most interesting.
Mitochondria are the source of many of the exceptions. The
endosymbiotic theory states that a bacterium was engulfed by an archaea and
they agreed to allow each other to do what they do best. These engulfed
bacteria became mitochondria and chloroplasts. But they didn’t always follow
the same path.
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We are finding that tRNAs can have multiple functions. 1-
This is the
usual route, the tRNA codes for an amino acid in a growing
peptide.
2- Some tRNAs code for the carry the same amino acid, but
have
differences in structure. The change in structure means they
don’t
bind the amino acid, so they are free to do other things. 3
and 4- These
non-aa bound tRNAs may be used for regulating expression of
specific
genes, usually in the end of the gene. 5- there are probably
functions
we don’t know yet.
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In animal and protist mitochondria, but
not plants, the stop codon UGA instead codes for the amino acid tryptophan.
You’d think that this would leave them with just two possible stop codons, and
some do. But in vertebrates, the codons AGA and AGG (usually code for arginine)
have been converted to stop codons. So we actually have four mitochondrial stop
codons.
Furthermore, animal mitochondria have switched up another
codon; AUA codes for methionine instead of isoleucine. In yeast mitochondria,
all the CU_ codons code for threonine instead of leucine. Again I ask… why? I
ask that a lot. Not so much why the genetic code has changed in mitochondria,
but why it hasn’t in plants. You
tackle that one on your own.
Nuclear genes have far fewer exceptions to the universality
of the genetic code. A protist or two have converted two stop codons to code
for glutamine, and the bacterium Mycobacterium
capricolum has converted the stop codon UGA to a tryptophan codon. Beyond
that, we have couple exceptions we have already discussed a bit, selenocysteine
and pyrrolysine.
The interesting story is selenocysteine (SeC). We said that it is coded for by a stop codon plus a special stem/loop structure downstream called the SECIS structure. This makes it the 21st amino acid. If it
is coded for, even indirectly, it’s going to need a tRNA. In this case, a
serine tRNA is modified in a two-step process to carry a SeC.
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These are two marine ciliate protist Euplotes crassus organisms
undergoing sexual reproduction, a marine ciliate protist.
They are
interesting for many reasons, but one is that they use a
slight
variation of the genetic code, and the other reason has to
do with
something called a frameshift. The codons are read in 3’s,
but some
genes in E crassus require
a shift in the reading frame to produce
the correct protein. This means that they go along a 3, 3,
3, 3, then
the ribosome has to move 1 nucleotide over, and then it
starts
reading 3, 3, 3, 3 again. The one nucleotide doesn’t code
for
anything, but must be there
to change the reading frame.
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The same group has a new paper that says humans can also end
up with cysteine in the Sec site (originally a UGA stop codon). How can these
two examples of cysteine in a Sec site take place, especially since the cysteine and SeC tRNAs
are completely different?!
It turns out that it's the levels of selenium and a
molecule called thiosulfate (SPO4) that is important for converting
other amino acids to cysteine. In some cases, the serine tRNA can be made into
a cysteine tRNA instead of a SeC tRNA. So here we have a case of a UGA stop
codon converted to a Sec codon then converted to a cysteine codon. Exceptional.
Next week, we can finish up nucleic acid exceptions. Do you think
A, G, C, T, and U are it when describing nucleotides? Not even close.
For
more information or classroom activities, see:
Genetic code –
Isodecoder tRNAs –
http://ymalblog.blogspot.com/2011/10/misfolded-human-trna-isodecoder-binds.html
