SStell

Thanks

So as the hydrogen ion is fueling the phosphorylation of ADP in ATP synthase it is being transferred from one protein to another and is really never a naked proton?

Thank you

When for example hydrogen ions are pumped against a chemical gradient and then used to power ATP synthase are these hydrogen ions naked protons or are they attached to a water molecule and form hydronium ions?

Thank you

Thank you That helps me understand the conversion between deoxyribose and ribose but are all NTPs phosphorylated by one type of ATP synthase or are there multiple types of ATP synthases?

Is there a protein complex embedded in a membrane that uses H+ to attach a phosphate group onto ADP for each of the 8 nucleotides? dATP, dGTP, dTTP, dCTP, rATP, rGTP, rUTP, rCTP? Or can you link me with some information in this regards? Thanks.

thanks

It is commonly accepted that 36 ATP molecules come from one glucose molecule. How is this number arrived at, determined, observed or experimentally verified?

Thank you for all your input. Just seemed to be a plausible and testable idea. More proof reading = less change, Less proof reading = more change. Could be epigenetic methylation silencing control of 'proof reading gene'. Different parts of the genome are effected differently. Thanks again. But natural selection probably does a fine job just on its own as Bender implied.

Hypothesis: There is some mechanism that functions to control the rate of mutation for DNA. Certain regions of the genome are allowed to mutate at a higher rate than other regions. Possibly in the proof-reading mechanism. More proof-reading versus less proof-reading. This would allow highly conserved areas to remain nearly intact generation after generation while other regions would change at the natural rate. Any ideas or data?

thanks, I think I am getting it

Babcock, So the electron would likely move from B to A. From low electron affinity to high electron affinity? Charon, So a photon is absorbed by a molecule (chlorophyll) which elevates an electron to a higher energy band, which then allows it to be transferred more easily to a molecule at a more negative redox potential with maybe some quantum tunneling to boot? And so on. So the electron itself is not the carrier of any extra energy but the atom or molecule it came from put that electron in that higher band and that and that alone allows the transfer to atoms of higher electron affinity? My whole confusion comes from the standard everyday diagrams of photosynthesis. They use the term 'energized' electron. I just didn't quite grasp that term. As electrons have no orbitals or energy bands or levels that I was knowledgeable of. I am wrong a lot so this would not be anything new. I usually understood a high energy electron as one with increased velocity as in particle physics etc. Kinetic Energy. So is this an example of higher chemical Potential Energy which allows it to then 'fall' down a cascade of proteins in the electron transfer chain?

So it seems that the electron is not carrying any 'extra' energy but is being placed into a higher redox potential spot by a molecule that gained its extra energy by just having the extra electron? It's not the electron but the molecule or atom that transfers the electron that has been 'energized'? I guess my query is about different energy levels or 'energized' single electrons. I just didn't think they did that. So it's the molecule or atom that has been 'energized' and not the electron. Or am I as usual completely confused?

thanks

That would be for an electron in an orbital energy level of an atom. If it is being transferred from one protein to another in some redox cascade how is this 'energized' energy being transferred. Is it in some alternate quantum state, because its velocity remains pretty slow. So it's not kinetic energy. I 'understand' energy levels in the atom etc. But I don't understand different energy levels of a single electron. Isn't an electron an electron an electron? Or is all about an electron being bumped up to a higher orbital in one molecular orbital which allows it to be transferred to a slightly lower energy orbital in an adjacent molecule and that transfer would be impossible from a lower energy orbital?

In the process of photosynthesis, electrons are 'energized' and injected into the electron transfer chain to eventually pump H+ into the lumen. What does 'energized' electron actually mean. Is the electron supposedly spinning faster, vibrating faster, or what? Because it cannot have its velocity changed. What exactly is an energized electron? And how is it different from a non-energized electron? Thanks

Emma, no one knows how the first cell was made, but there are quite a few folks trying to figure that out. A fairly large breakthrough along those lines was announced yesterday. Gerald Joyce et al developed a sequence of RNA that acted as an enzyme known as a ribozyme, well this new ribozyme can transcribe RNA and replicate RNA. What is special here is that this is the first ribozyme to have this ability, an ability once found just in proteins. Joyce is working on the RNA World Hypothesis. But more to your point, there are a few folks working on the Lipid World Hypothesis you might want to check out. Mycelles, microspheres, protenoids etc. are all possible precursors to 'cellular life". There is an interesting face book page dedicated to abiogenesis that may be of some interest to you.

thanks

In tRNA, rRNA, and ribozymes there are stretches of RNA that are bonded to compliments by hydrogen bonds and form helixes. There are also loops. Do the bases that form the loops have their hydrogen bonding regions facing outwards? I have attached a file to illustrate my question. Does the RNA naturally twist so that the bonding region is pointing outward?

Simon, """"If I am honest, I now think the title of the post wasn't a particularly wise choice because what I would really like to talk about is the emergence of life."""" WELL, get on with it already. Did you look into any of the many abiogenesis scientific hypotheses that I listed? Do you have any questions about any of them? Or are you just really here to see your own posts? Get on with it already. Seems someone is being quite insincere, but I guess- as they say, the proof is in the pudding.

Simon, you seem to be arguing just for the sake of arguing, you haven't actually said anything and have avoided answering any questions, how unique. Seeing as you really don't want to discuss your 'idea' I guess you really haven't thought it through. That is not how progress in a debate works. Good luck.

Simon, why don't we just cut to the chase already and leave the emotions and leading questions behind. What evidence do you have that supports intelligent design and what evidence is there for abiogenesis with its myriad hypotheses that you can refute with evidence? What experiments are intelligent design proponents actually doing that shows evidence for a designer and what experiments are biochemists doing that shows a natural process that you find fault with or can refute the findings of?

Life is just too complex for us to understand, therefore something much much much more complicated must have caused it. So Simon, the depth that you have researched your opinion is a really lame dictionary defintion and you chose the wrong part of that definition. Yikes!!!!! Might want to delve a bit further. Try the RNA World Hypotheis, Lipid world hypothesis, proteins first hypothesis, metabolism first hypothesis, panspermia and the list goes on and on and on. Of course you do need to give a complete definition for what you mean by 'life'.

The non-scientific theory of intelligent design: Cellular life is too complex for me to understand, therefore it is too complex for you to understand, therefore it is too complex for anyone to understand, therefore it is too complex for anyone to EVER understand, therefore god did it. Any questions?