[james oliver (OP)]

I asked the question earlier about what forces can break atomic bonds. I am ultimately trying to determine what can break the bonds of atoms , that make up the various essential amino acids (including bonds in R groups etc). Some folk curiously feel that amino acids are the most impervious, stable molecules/compounds on earth. I say leave that honor to diamonds (?).
  As i understand it, all it takes is for any one bond to "break free" from the collective if you will, for that particular amino acid, threonine say, to no longer be threonine.
  The trick part of the non trick question, is how can we break any of these bonds OUTSIDE of the human body's synthesis dynamics?
                                                                                                                                                                     Thanx  Oliver

[james oliver (OP)]

Same guy here; Is heat, the only thing that can break up a molecule? Can another atom or molecule breakup another molecule? I am referring to amino acids. I know that in the body matrix so many 'factors' can cause an amino acid to either decompose, or be modified (morphed into a derivative, but how can we do this outside of the body? how can we degrade, destroy, or change an amino acid?

[james oliver (OP)]

Same guy - I don't want to start a new thread topic each time, so this for now seems the best way to add on to the question/topic; Can the bonds in the amino acids that are in an egg say, be affected by the metal that is the pan? Copper, iron, lead etc. Can any of those metals, without the heat being turned on/up affect the bonds that make up and amino acid?  I don't mean the bonds that connect amino acids to each other to form a protein, but just the atom bonds that make up an amino acid.

[james oliver (OP)]

Whose leg i gotta hump to get some answers from this forum?

[CliffordK]

A little patience.  This is a forum where the majority of the people have an interest in science, but aren't employees of TNS.

Proteins can be relatively stable, even over very long periods.  Some researchers have discovered that demineralizing dinosaur bones can yield some dino proteins over 65 million years old.

You can think of chemical bonds as having different energy levels. 

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A relatively stable compound will take a significant amount of activation energy to push forward a reaction, for example oxidization of the bonds in an amino acid.  If the energy level of the products is greater than the reactants, then the reaction is endothermic, and will only proceed forward with the addition of energy.

You can make or break these bonds by adding energy in the form of heat, light (photons, perhaps UV), electricity, pressure, or one can lower the activation energy with the use of a catalyst or enzyme (which may also utilize chemical energy such as ATP).  Once the reaction is initiated, then more energy is recovered than what was put in if it is an exothermic reaction.

An amino acid is no different from any other carbon, or carbon-nitrogen compound.  It can be oxidized to generate energy (something that our body effectively does, creating ketones that are further oxidized to CO₂ + H₂O.  But, it requires activation energy to initiate the reactions.

As far as stable compounds.  Carbon Dioxide would have to be high up on the list, being at an energy minimum, although it will readily dissolve in water.

[Bored chemist]

While there are people here who could answer those questions I think the problem is knowing where to start.Perhaps your best bet would be to get a textbook or two.

However here's an answer to some of them.
"The trick part of the non trick question, is how can we break any of these bonds OUTSIDE of the human body's synthesis dynamics?"
There are lots of ways. Cooking food or burning things are probably the best known examples but any chemical reaction at all- say the rusting of iron- involves breaking and making bonds.
" Is heat, the only thing that can break up a molecule? "
No, light can do it too and so can electricity in certain circumstances.

"I know that in the body matrix so many 'factors' can cause an amino acid to either decompose, or be modified (morphed into a derivative, but how can we do this outside of the body? how can we degrade, destroy, or change an amino acid?"
Amino acids are just chemicals. They can react with things just like any other chemical.
Amino acids can, for example, be destroyed by bleach.

The direct reaction between the amino acids and the metal of the pan is unlikely- if it happened a lot we wouldn't use that metal to make pans from.



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[james oliver (OP)]

Hi
  Thanx for the reply's guys. I figured as much, that heat, light, certain if not all acids etc would indeed alter chemical molecules etc, but beyond seeking confirmation I was wondering if i might have some specific answers if possible; How much heat would be required or how much and for how long would exposure to light affect atoms and or whole amino acids etc?
  There were some things in your answers that I could wrap my head around - cooking temps, which we are all familiar with. And bleach. The different type metals is still an issue in that we, can't really see the chemical reactions that might be occurring when the egg is up against a certain metal pan - ??  -- unless someone has actually done those specific tests, first with a copper pan and then iron and then lead and so on and so forth. If anyone has done those type of studies where you examine the molecular makeup of an amino acid before resting it on the particular metals and then examine the structure to see if in fact it has even been slightly altered (protonated even???), that would be great and I would really be interested in those results. Unless i am on the wrong track with that one and the
"metal reaction" is more the interaction with other metals in the body or in minerals (which are both in and outside of the body).
  I  agree that aminos acids are "just chemicals", it is the "relatively stable" concept that leaves me wanting more specificity, as in relative to what? - not rendering the answer 'relative to weak bonds'  covalent VS ionic or hydrogen bond etc. which still provides little reference point for me.
  Besides bleach, are there other "household items" that might have a better chance at getting at chemical strructure of amino acids, like lemon juice or wine or even the stronger boozes that we use to cook with. I understand acetic acid is found vinegar for instance. We also use sodium hydroxide in plenty of food stuffs (ice cream thickener etc).
  Dimethyl sulfoxide is also found in many foods - can this play a role in oxidation of amino acids as well?
And final question (??); this idea of things readily (or not so readily - hydrophobic?) dissolving in water - is the dissolve dynamic a process in which things come apart, bonds break, and atoms go there separate ways etc?
  Thanx very much guys for clearing some things up and for future answers.   Oliver

[Bored chemist]

"Dimethyl sulfoxide is also found in many foods"
It shouldn't be.
Anyway, the bonds that hold together the atoms making up amino acids are covalent bonds.
I could look up the typical bond strengths in KJ/mol if it would help.

[james oliver (OP)]

Dimethyl sulfoxide (C2H6OS), or DMSO, is a sulfur-containing organic compound. DMSO occurs naturally in vegetables, fruits, grains, and animal products. It was stated on one site that Dmso can cause an oxidative loss of certain amino acids.
  Are all of the bonds that hold the atoms together covalent? Are there no ionic or hydrogen bonds? What about the side chains or R groups, are those bonds also covalent?
  I am focusing in on the 9 essential amino acids. Leucine, threonine, valine, etc
  Bored chemist et al - I am writing a book - it involves getting a cohesive understanding of how amino acids work outside the body processes and of course how we think they might work inside the body. The problem so far has been trying to get a consistent sense of the factors that can and do impact amino acids. Every source has differing facts and opinions.
  Some things should be without argument, like 2 plus 2 is 4, but for some reason with the amino acids some see them as diamond like, impervious entities, and many see them as "just" chemical compounds/molecules that fair no better or worse than any other. I agree with the latter but I have yet to put together a definitive picture as to how these 9 amino acids will react to certain criteria - heat, light, acids etc.
  At this point - a year and a half into research and writing, I am almost inclined to show the many arguments, and let the chemists have at it after publication. I have come to realize that perhaps the problem might be due to the fact that no one has really seen an amino acid at  work...inside the body, in real time. Proteins too for that matter. We can simulate body (stomach, liver) dynamics in vitro in a lab all day, with uber carefully controlled particulars.
  The human body doesn't work that way, and no two stomachs are alike (in terms of contents). So much of what really happens is based on assumptions of how chemicals react in a test tube. For that matter, have we really ever seen, "micro chemically", what happens when we create an elaborate brine with all manner of wine and lemon acids and salts and spices etc, and let a piece of meat (with all of it's own decay dynamics at work) marinate in it.
  Amino acids undergo myriad changes yielding scores of derivatives. We know this from lab work. None of these changes have ever been witnessed in real time in a real body - we just don't have the technology. We can see cell structure to some extent and cell damage as well, but proteins are way too small for even the most sophisticated instruments to see working in real live time in a body. Amino acids are even smaller.
  Your thoughts, and thanx for your input.   Oliver

[Bored chemist]

Trying to write a book on the reactions of amino acids without understanding the rest of chemistry is like trying to write a book on botany, but only looking at lupins.

Anyone who sees them as "impervious" should leave a bucket of urine around the place for a while.
The liver is very well versed in stripping the nitrogen off them  (as ammonia) and storing that as urea.
The kidneys are very good at moving that waste nitrogen out of the body and there are plenty of bacteria who are gifted at setting the ammonia free again.

There are plenty of differences between individuals, but there are a lot more similarities.
"For that matter, have we really ever seen, "micro chemically", what happens when we create an elaborate brine with all manner of wine and lemon acids and salts and spices etc, and let a piece of meat (with all of it's own decay dynamics at work) marinate in it."
Yes we have
http://en.wikipedia.org/wiki/Food_chemistry

[james oliver (OP)]

BC - I don't have to understand all of chemistry to have "a section" in my book speak to the inadequacies of chemistry. I checked out the link and as suspected it is still founded in theory or studies based on lab work:
"Food rheology is the study of the rheological properties of food, that is, the consistency and flow of food under tightly specified conditions", "Food chemistry concepts are often drawn from rheology,theories of transport phenomena..."
  By "inadequacies of chemistry" I don't mean to "diss" science, nor to expose science as fraudulent. My point is we have not really seen what happens to the molecular makeup or structure of many nutrients. Even in the food labs, there is a good level of science, but they are not really trying to gauge the damage done to nutrient molecules, in as much as they are figuring out ways to prevent spoilage or better understand fermenting dynamics and caramelization, and mallard reactions etc.
  What goes on in the body is radically different from what occurs in a lab - under "tightly specified conditions". No one has ever seen what a pill does when it enters the mouth. No one has ever seen what a banana does once it enters the mouth. There are plenty of writings about what can happen and what happens when organic matter meets up with salivary enzymes and then the other "juices" in the stomach and throughout the rest of the digestive process, but on a super micro micro level know one has ever actually seen the step by step process - how not just molecules but the atoms that make up the molecules do what they do in real, live time, in the body.
  We just don't have the technology for this. And while we are indeed more homogeneous than dissimilar as a species - it is still not enough to make an exacting assertion of "how things work". And it is this exacting issue that is key. It is this lack of exact science that yields a host of problems. This is why we have an increasing amount of "side effects" listed on drug labels. Each year, the list gets longer. The reason; each day some new person steps forth and says " I got this reaction from your drug...".
  What also gets longer is the amount of different maladies, pathogens, syndromes, diseases etc (12,000 to date). So much for being all alike.
  The fact that there doesn't even exist a picture/photo of a protein, in all it's structural glory, speaks to why i would question what chemistry knows about how proteins really work, exactly, or how they can be damaged. When we have the technology to see a real protein in action, and amino acids doing what they do (derivitating if u will), in real time, in a real body, then I would give better credence to any discussion of how things work.
   Then, we all would know the truth about nutrient damage, before we eat food and when the food is inside us. Then we would know to keep it simple perhaps; not mix this with that; lemons and milk say, or vinegar with spinach salad; meat on the grill, pasta in the boiling pot of water.
  Part of my book is to minimize if not do away with, speculation and conjecture. And the only way to do that is with actual tests that compare nutrient molecules before being introduced to certain criteria (light heat, humidity, oxygen, different Ph levels etc. and after.
   Once we are all looking at the same results, the conversation becomes less broad, less speculative with less conjecture, and zeros in on those realities of the altered molecule - which will be altered, and in most cases, irreversibly.
  If anyone on this forum has done these specific tests, that would be great, and I/we would look forward to your imput.

[Bored chemist]

"No one has ever seen what a banana does once it enters the mouth. There are plenty of writings about what can happen and what happens when organic matter meets up with salivary enzymes and then the other "juices" in the stomach and throughout the rest of the digestive process, but on a super micro micro level know one has ever actually seen the step by step process - how not just molecules but the atoms that make up the molecules do what they do in real, live time, in the body."
For a start they have.
http://en.wikipedia.org/wiki/Aspartate_protease

[james oliver (OP)]

I checked out the wiki link - close but no cigar. As we speak, I am efforting a meeting with some local NY chemists who might be willing to do a battery of before and after tests on various nutrient molecules. These test will be in vitro of course, which is sufficient for the one part of the study. Will keep all interested posted. Thanx again.

[Bored chemist]

Do you think that the reactions of that enzyme are different depending on whether it is in a laboratory beaker or someone's stomach?
If so, could you please explain how it knows?

[james oliver (OP)]

The reaction of any chemical will always be different in a lab than in the actual living stomach. All enzyme molecules are sensitive to their environment and to the other enzymes or chemicals, and single atomic elements they may come in contact with (salts, iron and other metals etc).
  In a lab we can put whatever we want into the equation and the amounts/ratios of each entity - and then watch and monitor and take notes. We have so little control and knowledge of exactly what is in any given stomach at any given time. It's not just the big things we ingest, it's all the combos of things and the differing infrastructure that each stomach creates over time.
  We don't have the technology to see each of the hundreds if not thousands of different atoms and molecules that exist and are created in the human body every millisecond - we just can't.
  We know in a lab, that a particular enzyme will react with AB and C in a certain way, but again that is a controlled situation. The reason drugs have so many side issues is because we don't know exactly what is going on inside the stomach or liver. The reason one person reacts to a food differently than the next person speaks to how truly dissimilar our innards have become. The reason some illnesses are hard to diagnose is because we cant really go inside and see what is interacting with what, and to reference lab dynamics falls way short of the truth and reality of what is happening in the human body.

[Bored chemist]

"The reaction of any chemical will always be different in a lab than in the actual living stomach. "
No, not really. The people who do this sort of thing are quite clever and they control for those sorts of things.
Also, at any particular moment the reactive site of the enzyme simply isn't big enough to have many "other things" in it to affect it.

"We don't have the technology to see each of the hundreds if not thousands of different atoms and molecules that exist and are created in the human body every millisecond - we just can't."
Why would we need to?

"The reason drugs have so many side issues is because we don't know exactly what is going on inside the stomach or liver. "
No, we quite often know exactly what's going on.

[james oliver (OP)]

Bleeding, a rise in bad cholesterol, joint pain, arthritis, headaches, rashes, joint and muscle pain, dry mouth, nausea, blurred vision, constipation or diarrhea, dizziness, fatigue, weight gain, anxiety, hyperactivity, hostility and agitation, loss of sex drive, too much sex drive and an overly extended erection, impairment of the kidneys, liver, or urinary tract; increased risk of bone fracture, suicidal tendencies (including risk of suicide in children), increased sensitivity to sun exposure, weight loss, decreased appetite, nervousness or confusion, allergic reactions, heart palpitations, seizures, fatigue, dilated pupils, sexual dysfunction, sleepiness, increased sweating, increased blood pressure, lightheadedness, dry mouth and nose, impaired cognitive abilities, Severe allergic reactions ( hives; difficulty breathing; tightness in the chest; swelling of the mouth, face, lips, or tongue); confusion; depression; fast heartbeat; hypothermia (fast breathing, shivering) – oh, and death.
  BC - these are just some of the things that can go wrong inside the body - just some of the chemical reactions that can't be precisely foreseen. The reason we know about any of these side effects is not through lab study but because people coming in and saying I took this pill for one thing and then this other thing happened. Science then writes this down and adds it to the list of things can MAY happen. They still have to say may on the labeling or commercials because they are not sure... because they can't really see inside the body and know what is truly and precisely and specifically going on. It is the exactness that is lacking - because we don't have the technology - and we may never have that level of technology - it will always be a guessing game and man and science will always be behind the 8 ball because the human body is ever changing, mutating, due to diets, environmental conditions, genetics, and genetic blends when to people make a baby and so on and so forth.
  Scientists are quite clever but never as smart as mother nature. If we were, so many diseases would have been eradicated by now (or at least preventive measures that are foolproof - we can't even do that for the common cold) - instead we're going in the opposite direction - we have 12,000 diseases to date and more cropping up each year.
  If we were truly smart enough to know exactly what is going on, we would be able to correct so many of the problems. Like a car mechanic who truly knows exactly what is wrong with a car - and can fix it.    Oliver
                                                             
                                                         **DMMP

[Bored chemist]

What a long and pointless list.
I know things go wrong.
What you won't accept is that in many cases the causes are actually known at the molecular level.
That's why we are able to treat a lot of conditions.


It's called rational drug design
http://en.wikipedia.org/wiki/Drug_design

[james oliver (OP)]

I am not saying we don't know what happens at a molecular level - labs show us that. Again, I am referring to not knowing exactly, as in precisely, everything, that happens the instant you put anything into your mouth, be it a drug or a food (all chemicals still).
  We don't have the technology to see and follow every uber subtle, microscopic dynamic, that goes on in the body as it is happening. If we could, we could follow something along it's path and see and identify the exact precise point at which it took a 'turn for the worse' (the bad reactions that we had, say) .
   Won't u won't accept is that in many more cases, the causes are not known at the molecular level, and that is why we can treat a lot less conditions that than the millions that we can't treat.
  Rational drug design has way to much guess work still - it's the only industry that can get away with such ineptness (that and politics).
   It's the only industry that can get away with "this might work" or "lets try this" or.... "you can't sue us when stuff goes wrong cause we already listed a bunch of things on the label that might go wrong so we're covered, and each year we'll add to that list cause we're still guessing, cause we don't have the technology to really see how any of this stuff really works in real time, in real body dynamics, so we don't really know , so we'll just keep throwing stuff on the wall till something sticks, and our insurance will continue to rise but we are super rich (Pfizer) so we don't really care, and while we're at it we have a website dedicated to giving your pets drugs too (google it), cause they can't complain or sue and they are just as naive as the ignorant human masses who fill our coffers each year and haven't yet figured out that we don't really have a clue about how to heal folks, and most of our products might as well be placebos, except that placebos don't have side effects that include death like 70 percent of the drugs we give people.................. In the spirit of long and pointless.

[Bored chemist]

We largely know what the "turns for the worse" are at the molecular level.
It's more often at the cellular level that we don't know.

"It's the only industry that can get away with "this might work" or "lets try this" or.... "you can't sue us when stuff goes wrong cause we already listed a bunch of things on the label that might go wrong so we're covered,"
No, not really,have you ever read the end user agreement on any software?
And quite a lot of medicine is in that position- not just pharmacology.

"while we're at it we have a website dedicated to giving your pets drugs too"
Are you saying that sick pets shouldn't be treated?