 |
| Fig. 1 DNA to mRNA to Amino Acids to Proteins-with-Sulfur |
This series considers the atoms of proteins.
There is no sulfur in DNA or in mRNA nucleotides, but when the ribosomes receive an mRNA message made from the cell's DNA (then sent from the cell's nucleus out to the cell's outer cytoplasm realm) any ribosome receiving that mRNA will add some amino acids (which contain sulfur atoms) to the ongoing protein mix.
Where the ribosome got the sulfur is not the only consideration in this series, because how the ribosome came to be is a mystery too.
The question "how did the ribosome become an astronomical number of atoms working in concert?" comes to mind as well (On the Origin of the Genes of Viruses, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18).
Mysteries like those engender anything from hypotheses to fables categorized by Latin speaking nomenclature authorities which are placed into the realm of Teleology:
“Teleology is like a mistress to the biologist; he dare not be seen with her in public but cannot live without her.” —J. B. S. Haldane
(emphasis added, On The Origin of The Containment Entity, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16).
That evidently started in "the year of the cat", which is still with us (On The Origin of The Containment Entity - 8), because:
"... teleological causality [in atomic structures] implies the ability to imagine and plan for a future state of affairs, an ability that can only exist within a mind or some other kind of nonphysical or transcendent reality..."
(The History of Teleology in the Biological Sciences, p.6 ). The "year of the cat Latin speaking scientists" still teleologically put it like this:
"Methionine and cysteine may be considered to be the principal sulfur-containing amino acids because they are 2 of the canonical 20 amino acids that are incorporated into proteins ... Why does nature [the mistress] employ sulfur in her repertoire of amino acids?"
(The Sulfur-Containing Amino Acids: An Overview, emphasis added). Of course the doll big mama nature does it because, among other things:
"Substitution of oxygen for sulfur in S-adenosylmethionine would produce so powerful a methylating agent that it would promiscuously methylate cellular nucleophiles without the need for an enzyme."
(ibid, emphasis added). Don't you love it when scientists 'talk dirty'?
Mama mistress does not want any promiscuity going on in the daytime else the imaginations of her suitors in strictly scientific circles would seem to be impolite.
But I digress, so let's remember that the ribosome is an atomic scientist of the highest order:
"Because both sulfur and oxygen belong to the same group (Group 6) of the Periodic Table and, therefore, are capable of making similar covalent linkages, the question may be restated: why would methionine and cysteine analogs, in which the sulfur atom is replaced by oxygen, not serve the same functions? One of the critical differences between oxygen and sulfur is sulfur’s lower electronegativity. Indeed, oxygen is the second most electronegative element in the periodic table. This accounts for the use of sulfur in methionine; replacement of the sulfur with oxygen would result in a much less hydrophobic amino acid. Cysteine readily forms disulfide linkages because of the ease with which it dissociates to form a thiolate anion. Serine, on the other hand, which differs from cysteine only in the substitution of an oxygen for the sulfur, does not readily make dioxide linkages. The difference results from the fact that thiols are much stronger acids than are alcohols, so that the alcohol group in serine does not dissociate at physiological pH."
(ibid). In other words, the why of adding a couple of sulfur atoms to avoid promiscuity down the genetic road isn't understood as well as it could be, but who's counting?
Which brings us to the continuum of constants not only in the DNA but also in the RNA (On The Origin Of A Genetic Constant, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, On The Origin Of Another Genetic Constant, 2, 3, 4).
But that is not the end of the matter, no, there is yet another constant in the proteins that result after the ribosomes do their thing.
The proteins made by the ribosome have vestiges of the constant that exists in the ACGT and U nucleotides, which is an atomic discovery (Atomic Model of the Thermus thermophilus 70S Ribosome Developed in Silico).
These atoms were first described almost a century ago as:
"About a hundred years ago, eugenicist journals reviewed books concerning the notion of how eugenicists should contemplate atoms, in whole or in part, when the subject of consciousness was being related to atoms:
'At this point the theories of philosophical physics are brought into the hypothesis. Matter is composed of electrons and protons, forming atoms and molecules which are themselves separated by the ether and through which, though widely spaced apart, they act upon one another. Protons and electrons are only modifications of the other. Thus matter being itself etherial can act upon the ether; and the cortical nerve endings, being material, set up etheric vibrations which are sent out radially through the ether, without the necessity of any definite paths.'
...
'Provided there be a psychic organ capable of picking up these vibrations and responding to them, capable also of emitting etheric vibrations to which the material brain will respond, we have an explanation of the possibility of Interaction. But what is to be the nature of the psychic organ thus postulated? Like the material brain, formed of protons and electrons, the psychic brain will also be formed of derivatives of ether, 'of etherial units of a finer order which may be called psychons. The structured protoplasmatic brain
will have its counterpart in a psychoplasmic structure. Moreover, since protons and electrons which constitute protoplasmic structure are widely spaced apart there is no difficulty in the way of a conception of an interpenetrating psychoplasmic structure.'
...
'Tomorrow you will scarcely find a man who is up to the greatness of the new tasks, and I venture to say that the very best of our own time have not discharged themselves any too well of the difficulties they have encountered. The mass of knowledge which is now required exceeds our capacity for understanding. The time is no longer when everything was explained by the immobile and indivisible atom, by the cell and karyokinesis, transformism, gravity and Euclidian geometry. Science now is bordering on the infinite and the most powerful brain feels feeble in front of the tasks which are glimpsed.'
...
'Darwin's speculative gemmules of the nineteenth century have become the experimentally demonstrated genes of the twentieth century, and the reality of their existence in the cell is now as certain as that of the electrons in the atom. The fundamental importance of the gene in biology is certainly as great as that of the electron in physics and the atom in chemistry.'
...
'... the mechanistic view of life - that is the view that what we call life is merely the result of the spatial arrangement of certain atoms and molecules. Here he has the mechanists at his mercy, for as a professor of physics he is pitilessly severe on the bad physics and worse chemistry of the mechanistic biologists. In America the mechanistic view is rampant, in England and Europe generally it is being silently abandoned by the more thoughtful biologists.'
...
'The principle is not limited in this treatise to the organic world, but begins with our present theories of matter and force; and Smuts shows clearly how the combination and interaction of a group of electrons forms an atom which, as an entity, has wholly new and wholly different characters from the individual components. Thus the integration or combination of units gives something new. This is 'Holism.' The theory is carried through a series of inorganic forms to the organic, and reaches finally the evolution of man, and the evolution of society and societies. To the evolution student it provides a most helpful conception, and one would think that to most men this is one which should easily dispel all those confusions of thought which lead to our present-day controversies on the possible reconciliation of evolution beliefs with theistic and spiritual ideas about the universe.'
(The Eugenics Review, emphasis added; cf. PDF). So, 'wholly new'" and 'wholly different' electrons and protons were interested in making atoms and then contemplating how they could then change them via an atomic natural selection perhaps?
(Small Brains Considered - 16). No, it is not exclusively 'yesterday', because we find that there is still a wide array of beliefs about the intelligence of atoms in the scientific community today; get your psychons on dude.
For example, evolution is not only seen as a lethal mutation (What Kind of Intelligence Is A Lethal Mutation?), it is also seen as a central location of some psychon religious beliefs:
"... Roger Penrose and I have developed a theory of consciousness ... It basically proposes quantum computation in brain neuron microtubules inside neurons. So rather than neuron-to-neuron communication, we're looking at a deeper level inside neurons to give a global sense of consciousness through quantum mechanics, which results in real-time causality and free will ... it gives consciousness real-time control and a potential connection to fundamental space-time geometry, quantum space-time geometry, through Roger's objective reduction. This is consistent with Eastern spiritual traditions. Although Roger doesn't like to talk about it, I've taken the liberty of observing the implications of what he said and what we've said for consciousness, for Eastern philosophy and other spiritual traditions ... if quantum consciousness is correct, for example, if Penrose's idea is correct, we are literally ripples in the fine structure of space-time geometry, which can resonate - levels of consciousness can resonate from the Planck scale, the bottom level of the Universe, multiple hierarchical levels to the brain. This is consistent with Eastern philosophy and also indicates that afterlife, reincarnation, and out-of-body experiences that we've heard about are plausible. The quantum soul."
(Small Brains Considered - 6). Whatever happened to the art of the hypothesis; specifically the part where the scientist making a hypothesis must also provide a "how to falsify this hypothesis" method (Falsifiability)?
But I digress.
In the next posts of this series, over the next year I suppose, there will be a bazillion proteins of various organisms (in up to 589 appendices) analyzed at the atomic level as has been done with DNA and RNA in multiple previous series on Dredd Blog.
Here is a link to a tease appendix to give readers a sense of coming events (Appendix Index).
It is in "Appendix : Organism" order; "Appendix" meaning the appendix file number, and "Organism" meaning the taxonomic nomenclature of an organism or organisms featured in that appendix file.
Take a look at the "Appendix Index" and you will see that there is a train load of protein atom data coming for readers at various times over the next year.
The upcoming posts in this series will have details about proteins in that organism's DNA -> mRNA -> Amino Acid ->Protein sequence (from nucleus DNA to mRNA to ribosome in eukaryotes and a bit more simply in prokaryotes).
I have already written the software that generates the appendices after analyzing the proteins; however since there are too many appendices to do in one post, so it will probably take many posts to cover the topics involved.
Let me start with the facts that: 1) the same proteins are found in a diverse array of organisms 'alongside' unique proteins inside that organism; 2) that "proteins are essential parts of organisms and participate in virtually every process within cells"; and, 3) they are made of only one more atom type (sulfur - see Fig. 1) than the four atom types which nucleotides ('A', 'C', 'G', 'T', and 'U') are made of.
The ribosome is the 'brain' of the show, so the Dredd Blog "Small Brains Considered" series will be referred to from time to time (Small Brains Considered, 2, 3, 4, 5, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17).
Let's get started with beginning appendices (A001, A002, A003, A004, and A005).
Note that at the bottom of each appendix is a "Totals For Protein List Above" section that has, in addition to the atom counts and relevant constants, a link to the GenBank data of the organism which the proteins came from.
Note also that there is a unique id for each protein, which you can paste or type into the GenBank look-up page to retrieve the data relating to that protein.
The next post in this series is here.
A polymath speaks at Harvard:
