UV Absorbance difference between Purines and Pyrimidines
Tom Hendricks
http://matcmadison.edu/biotech/resources/methods/labManual/unit_4/exercise_15.htm
"Most biological molecules do not intrinsically absorb light in the visible range, but they do absorb ultraviolet light. Biologists take advantage of UV absorbance to quickly estimate the concentration and purity of DNA, RNA, and proteins in a sample... It is also possible to quantify the amount of DNA in a sample by looking at its absorbance at a wavelength of 260nm or 280nm (in the UV region)...
Proteins have two absorbance peaks in the UV region, one between 215-230 nm, where peptide bonds absorb, and another at about 280 nm due to light absorption by aromatic amino acids (tyrosine, tryptophan and phenylalanine). Certain of the subunits of nucleic acids (purines) have an absorbance maximum slightly below 260 nm while others (pyrimidines) have a maximum slightly above 260 nm. Therefore, although it is common to say that the absorbance peak of nucleic acids is 260 nm, in reality, the absorbance maxima of different fragments of DNA vary somewhat depending on their subunit composition. "
What if UV is a selective force at the start of life. If purines, and pyrimidines have slightly different absorbance maximums, then wouldn't each have a selective advantage under certain UV conditions?
Thoughts?
Tom Hendricks
Cory Albrecht
Does anybody know what the absorbing spectrum of a the primeval,
non-oxygenated atmosphere would have been compared to our atmosphere
today?
Alan Meyer
> ...
> What if UV is a selective force at the start of life. If
> purines, and pyrimidines have slightly different absorbance
> maximums, then wouldn't each have a selective advantage
> under certain UV conditions?
I think the answer to this question is an unequivocal No, at least
for DNA based life forms.
Every DNA base pair contains exactly one purine and one pyrimidine.
If UV light were deleterious to either one of them it would
have the same negative effect on DNA, destroying the same set of
base pairs.
Alan
Tom Hendricks
> Tom Hendricks wrote:
> > ...
> > What if UV is a selective force at the start of life. If
>
> =A0> maximums, then wouldn't each have a selective advantage
> =A0> under certain UV conditions?
>
> I think the answer to this question is an unequivocal No, at least
> for DNA based life forms.
>
> Every DNA base pair contains exactly one purine and one pyrimidine.
> If UV light were deleterious to either one of them it would
> have the same negative effect on DNA, destroying the same set of
> base pairs.
>
But at the start of life we had a strand of RNA. What if the UV was
such
that it was most dangerous to purines? Then we would have an
RNA pyrimidine world. Or depending on how the RNA folded, there
would be vulnerable purines at the ends so damaged by UV that they
could not fold
or react properly.
Look at a tRNA. I think you'll see a structure that is in many ways a
response to
UV. Think of pyrimidine dimers and how that could effect the origin
and coding.
If purines and pyrimidines both have differences
two hydrogen bonds versus three
different UV absorbance
then that must account for some selection differences.
Lorentz
> This excerpt from MATCMadison,edu on absorbing UV light.http://matcmadiso=
n.edu/biotech/resources/methods/labManual/unit_4/exe...
Yes, I think that the damage due to UV light on biological molecules
exerts a great deal of selective pressure on organisms that are
regularly exposed to UV light. However, I think that life could arise
in a world that never had any UV radiation.
>
> Proteins have two absorbance peaks in the UV region, one between >215-230=
nm, where peptide bonds absorb, and another at about 280 >nm due to light =
absorption by aromatic amino acids (tyrosine, >tryptophan and phenylalanine=
).
The damage done by UV radiation is not solely determined by the
absorption spectra of biological molecules. The proteins are excellent
examples of materials where the damage done by electromagnetic
radiation is not solely determined by absorption spectra.
If UV light is absorbed by the peptide bond (215-230 nm), the
peptide bond will probably break. The peptide band is not stablized by
any electronic resonance. All protein molecules have an absorption
band between 215 and 230 nm. So any protein regardless of amino acid
content will be degraded by UV light between 215 and 230 nm. The
absorption by the peptide bond also results in very little
fluorescence or phosphorescence emission. The peptide bond falls apart
before the electron can emit photons or phonons. Sometimes the broken
bond forms a free radical, that can damage other molecules. So
absorption between 215 and 230 nm can be lethal.
In fact, any substance with a double bond is likely to
decompose when exposed to UV between 215 and 230 nm. Almost every
biological molecule has double bonds somewhere in it. So it is very
likely that the first living things evolved in the absence of UV
between 215 and 230 nm.
UV radiation between 215 and 230 nm could never reach the
surface of any planet with any reasonable atmosphere. I am not just
talking about ozone (i.e., triatomic oxygen). Diatomic oxygen and
diatomic nitrogen would absorb this radiation. Carbon dioxide would
absorb this radiation. Water vapor absorbs this type of radiation. I
can imagine a very thin atmosphere of methane, hydrogen and argon
letting through some of this radiation. However, I can't imagine
anything under liquid water being exposed to this sort of radiation.
So we are left with a planet similar to Mars. If you have a mechanism
for abiogenesis applicable to the CURRENT conditions on Mars, then you
should contact NASA with this theory.
The absorption peak near 280 nm is not associated with
photodecomposition. Aromatic amino acids are associated both with the
peptide band and another band located in the benzyl ring. The benzyl
ring is very stable due to aromatic resonance. Thus, when the benzyl
ring is excited the aromatic bonds do not break. Much of the energy of
the excited electron either goes into fluorescence emission,
phosphorescence emission, or energy transfer to another nearby amino
acid. Very little absorption by the aromatic band results in a bond
breaking down. So the aromatic amino acids are very strong
fluorophores relative to other amino acids.
When a benzyl ring is excited in a protein molecule, it is very
likely to transfer its energy to another benzyl ring. When an aromatic
amino acid is excited in a protein molecule, the energy tends to jump
around. Amost all the energy absorbed by any of the three aromatic
amino acids (tryptophan, tyrosine, and phenylalanine) ends up in
tryptophan. Regardless of which aromatic amino acid absorbs light, it
is the tryptophan that eventually receives the energy. Therefore, if
absorption by UV radiation at 280 nm and shorter where important, the
tryptophan is the first to go. When that tryptophan is broken down,
the entire molecule is likely to stop working. Tryptophan is one of
the most common amino acids. It is in fact the main reason proteins
fluoresce. The emission band of proteins at 340 nm is primarily
tryptophan.
It is possible that tryptophan helps protect other amino acids in
the protein molecule from UV damage. However, one would expect
tryptophan to be at sites in the protein molecule which are not vital
to function. I never heard of such a preference.
>Certain of the subunits of nucleic acids (purines) have an >absorbance max=
imum slightly below 260 nm while others >(pyrimidines) have a maximum sligh=
tly above 260 nm. Therefore, >although it is common to say that the absorba=
nce peak of nucleic >acids is 260 nm, in reality, the absorbance maxima of =
different >fragments of DNA vary somewhat depending on their subunit >compo=
sition. "
Under current conditions on earth, UV at 260 nm doesn't reach the
surface of the earth. It most certainly never reached the bottom of
the oceans. However, suppose it once did.
> What if UV is a selective force at the start of life. If purines, and pyr=
imidines have slightly different absorbance maximums, then wouldn't each ha=
ve a selective advantage under certain UV conditions?
the sunlight contains UV between 250 and 300 nm. I am basing this an
the cutoff frequency of diatomic oxygen, which starts at about 250 nm.
This spectrum is very broad. A small difference of say 5 nm won't make
a significant selective difference. Every nucleotide and every amino
acid would be almost uniformly. An argument made for proteins also
applies to DNA. The energy, even if the difference were significant,
will go to the lowest energy nucleotide whatever that is. So
basically, the small differences in absorption spectrum won't make a
difference.
>
> Thoughts?
Those are my thoughts. Don't kill the messenger. I am just trying
to help.
Lorentz
> If purines and pyrimidines both have differences
> two hydrogen bonds versus three
> different UV absorbance
> then that must account for some selection differences.
Only if the difference absorbance corresponded to different
photodecomposition. Some chromophores can absorb radiation without
decomposition. The benzyl-ring chromophore in aromatic amino acids is
an example of a chromophore that absorbs UV without a corresponding
decomposition. I suspect that the pyradine-ring chromophore in
pyradines is the same way.
In many posts you repeat the assertion that
absorption=3Ddecomposition. This is not always true.
Also, you do realize that a lot of chemical environments break
down double bonds without UV radiation. In fact, some chemical
processes break down the double a lot better than UV absorption. The
differential selection that you ascribe to UV may be instead caused by
a high or low pH.
You also have this belief that the only seasonal change
possible are changes in UV irradiance. Seasonal cycles, even though
originating in the sun, express themselves in different ways. The
seasonal cycle could, for instance, cause an oscillation in pH. Even
if you think oscillations are necessary for abiogenesis, and I do not
believe so, the oscillations can be due to changes in the chemical
environment.
Maybe the surface where life started was near a beach, which was
periodically covered with salt water by the tide. A dry-salt water-dry
cycle twice a day. Or maybe once every 15 days, as happens wide
supertidal zones. Then the cycles would be associated with the moons
gravity. The cycle, if you need one, may not be solar at all. It
certainly doesn't have to involve UV. It very well may involve solar
UV, but it doesn't have to.