Re: UV Absorbance difference between Purines and Pyrimidines

On Sep 16, 12:34=A0pm, Tom Hendricks <tom-hendri...@xxxxxxx> wrote:
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?
No. I can imagine a world without ozone (triatomic oxygen) where
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.

.

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