[Olivia james]

Hi this might be reposted (i think i hit post twice)
 Borek, it has to matter for nutrition. This is the disconnect I am trying to do away with. A molecule is a molecule is a molecule. We can't have it both ways. With the exception of minerals perhaps, all nutrients are molecules. If we establish that premise, then the next premise to establish is that molecules formed can be unformed when exposed to various criteria (other molecules, light heat, Ph, oxygen etc.)
  If we can damage the bonds that link one amino to another to form a peptide or protein, then we can also affect the bonds that link one atom to another to form an amino acid. If there is another established premise (at least in this thread), that the removal of one or more atoms from the amino makes it something other than the original amino, then I am indeed affecting the nutrient molecule rendering it not a nutrient. It may have been thus converted to another molecule/amino but not the one I had intended to ingest.
  There needs to be some consistency here. We cannot dismiss cooking dynamics from regular natural atmospheric or lab created dynamics that alter amino molecules.
  Dr cms - you are in agreement that the molecule/amino is altered but put forth that it can still be used as fuel. If we affect the amino to the extent that all its bonds have been broken and all the atoms have been left on their own, made separate, then what we have is nitrogen, oxygen, carbon, hydrogen floating around - and we have that already in the atmosphere.
  Amino synthesis , organically, suggests the perfect storm is required to get these particular aminos and that it is not just a random gathering of atoms. To break those bonds and expect them to reconvene at a later date (in the digestive process) seems counter to the idea of specific and complex amino synthesis.
  I have moved beyond the protein thing and how we can affect them by introducing certain criteria - external forces. It is the death of an amino that needs to be determined. At some point that damaged and or destroyed amino can't still act as fuel. It makes little sense that aminos are impervious to complete destruction. Even atoms on their own can be affected, albeit by extreme forces. But compounds of elements/atoms are far easier to breakdown. And again, we have the premise that once you've broken down the amino , Threonine say, it is no longer Threonine (the nutrient Threonine).
  BTW our brain size was most likely increased by the increased intake over millennium, of carbs. 20 thousand years ago we didn't consume wheat products (pasta, bread etc) or corn, or beans or rice, or potatoes like we do today.
  Overall I get that each amino has different destruct levels if you will - that's what I'm looking for; that list, that study based list that says these 9 essential aminos are affected in this and that manner. What I get from food science and mass marketing is a generic, homogeneous approach to proteins and aminos which is curious to begin with; milk protein is different from egg and soy and wheat protein etc

[Olivia james]

This is in reply to fledarmus; I get that the proper term is amino acid (just bad habit). Perhaps in a chem forum that mistake is more critical than in most other forums. Moving on. I also get the protein is formed by AA's and that the AA's will then do what they are intended to do in the body, in the digestive process and other biological processes.
  I am talking specifically and solely about the amino acid before it enters the body. What criteria can affect the AA and to what extent and how. This is all i am trying to determine. Internally, AA's are affected by a multitude of factors that modify them, and or allow them to join forces with other AA's to create new proteins etc, or just act as free amino acids.    Which of the many factors internally that affect an AA, can and do exist outside the body? There has to exist, the dynamics of oxidation, Ph, photo/light issues. as well as heat, that impact for better and for worse these amino acids outside the human body. I am trying to get a handle on a least some of those dynamics that affect an AA before ingestion.

[Borek]

If we can damage the bonds that link one amino to another to form a peptide or protein, then we can also affect the bonds that link one atom to another to form an amino acid.

These are different bonds and they behave differently.

There needs to be some consistency here.

There is a consistency here, but to see it you need at least some introduction to GenChem 101 and BioChem 101. This thread is going nowhere as you are trying to apply your misconceptions about the basics to the behavior of the more complicated system. It won't work.

[Olivia james]

I don't have any misconceptions. I also don't have any specific answers. I know that each amino acid is different and with different bond dynamics and particulars. All I am asking for is the nine essential amino acids to be explained in terms of how they can be damaged (made completely useless) by various forces, light heat oxygen, Ph etc - outside the body.
   Lets take Threonine or lysine or Valine. Lets take anyone of these and explore what can affect them - out side of the body. Certainly if we dipped Valine in to a jar of vinegar or lemon juice something is going to happen. I can't tell what is happening in my kitchen because i don't have the tools/instruments or knowledge and skill set to tell you just how the molecule that is the amino acid Valine has been changed - making it no longer Valine.
  I don't have to have years of chem study to ask you to tell me what you may or may not know. If someone in a lab works with Valine daily (or monthly?) they would be quick to tell me XY and Z about Valine and all of it's components and what forces can alter it's components etc. They would say don't do this or else; they would say, if you introduce ammonia perhaps to the equation, this will happen - and so on and so forth.
 If you borek don't know these particulars that i am asking then it's is okay - i will continue to seek out the chemist that does. Everyone has their particular fields of expertise. If you work with the amino acid Lysine for instance for the industrial purpose in grain feed say, you're going to know everything about it. You are going to be working with Lysine out side of the body and will be able to identify what forces can enhance, modify or damage Lysine. This is what i'm looking for - this is what i want to know. As I'm writing this, i'm thinking maybe i could ask someone who works with lysine, and go on down the line to find people who actually work with any or all of the specific 9 essential amino acids.

[discodermolide]

I don't have any misconceptions. I also don't have any specific answers. I know that each amino acid is different and with different bond dynamics and particulars. All I am asking for is the nine essential amino acids to be explained in terms of how they can be damaged (made completely useless) by various forces, light heat oxygen, Ph etc - outside the body.
   Lets take Threonine or lysine or Valine. Lets take anyone of these and explore what can affect them - out side of the body. Certainly if we dipped Valine in to a jar of vinegar or lemon juice something is going to happen. I can't tell what is happening in my kitchen because i don't have the tools/instruments or knowledge and skill set to tell you just how the molecule that is the amino acid Valine has been changed - making it no longer Valine.
  I don't have to have years of chem study to ask you to tell me what you may or may not know. If someone in a lab works with Valine daily (or monthly?) they would be quick to tell me XY and Z about Valine and all of it's components and what forces can alter it's components etc. They would say don't do this or else; they would say, if you introduce ammonia perhaps to the equation, this will happen - and so on and so forth.
 If you borek don't know these particulars that i am asking then it's is okay - i will continue to seek out the chemist that does. Everyone has their particular fields of expertise. If you work with the amino acid Lysine for instance for the industrial purpose in grain feed say, you're going to know everything about it. You are going to be working with Lysine out side of the body and will be able to identify what forces can enhance, modify or damage Lysine. This is what i'm looking for - this is what i want to know. As I'm writing this, i'm thinking maybe i could ask someone who works with lysine, and go on down the line to find people who actually work with any or all of the specific 9 essential amino acids.

Take your last example, lysine. If you enhance or modify it it is NO longer lysine. If you "damage it" chemically it is no longer lysine.
The same goes for all the other amino acids.
That's it there is no other answer.

[fledarmus]

Your answer is different for every single amino acid and for every single protein. These are all different compounds, and they react differently.

For the most part, amino acids are relatively stable compounds. Valine is particularly stable; the side chain is a simple isopropyl group. All that can really react in this molecule is the amine and the carboxylic acid. Vinegar and lemon juice are acidic enough to protonate the amine, but nothing else will happen. The valine will just sit there in the vinegar solution. Add enough sodium bicarbonate and you will neutralize the amine and deprotonate the carboxylic acid.

Lysine has a 1-butyl-4-amino sidechain, giving it an extra amine. Again, the only thing that is likely to happen in vinegar is that it will protonate both amines.

The amide bonds between amino acids in a protein are more reactive - in the presence of strong acids or strong bases, you can break those amide bonds and release free amines. Since organisms rely so heavily on amino acids, there are many enzymes which will also cleave amide bonds, some in very specific positions that recognize particular strings of amino acids, and some in a much more general sense that will cleave almost any amide bond. This is what happens in your stomach. This is also what happens in certain marinades; papain is used frequently as a meat tenderizer because it cleaves a number of the peptide bonds without completely digesting the protein.

As far as what modifying amino acids chemically will do to its use in the body, that depends entirely on the amino acid and what you do with it. The natural amino acids are pretty stable - for the most part, you have to do things like actually burn them to change them chemically to the point where they can no longer be used as amino acids by the body. No, humans do not make food out of carbon dioxide and water; that is photosynthesis. We are higher up the food chain - we have to rely on other organisms to produce more complex organic molecules for us to use in our own biological processes.

Yes, almost anybody with a year of organic chemistry can look at the structure of a lysine molecule and predict all sorts of reactions that it would undergo. Almost all of them require either laboratory conditions which you are not interested in, or bioorganic conditions which would require you personally to commit yourself to a few semesters of advanced college biology and/or chemistry courses (or the equivalent in self-guided study) to ground yourself in. Without a better idea of what it is you are trying to figure out and for what purpose, I can't tell whether you're asking something incredibly simplistic and we just can't understand your question, or whether you're asking fundamental questions of biology and we would need to respond with a thesis to even begin to answer.

If you're really serious about trying to understand the role of amino acids in organisms, go to either wikipedia or google scholar and start looking at some serious work on the biosynthesis, transport, and recognition of the specific amino acids you are interested in. A preliminary course in protein synthesis would also be helpful to you.

[Olivia james]

Fledarmus - I am not trying to understand Amino acids in organisms. You're right, I can google that. What i can't google, yet, is how each each of the 9 essential aminos acids can be altered out side of the body matrix.
  discodermolide was on the right track as to what I am trying to get at, which was already established some time back in this thread; remove one atom, or enhance, modify or damage the amino acid chemically and it is no longer that particular amino acid with that specific function.
 What I am still searching for is what exactly, precisely, will affect each of the nine, as regards to heat, Ph, light, oxygen etc. to make it no longer that amino acid. Relatively stable doesn't really help, unless i know what it is relative to. Everything is "stable" until it's unstable, and the degree of stability will always be relative to something else. I am trying to eliminate generalities and hone in on specific occurrences, in specific scenarios, with specific variables/criteria.
   Specific. Architecture deals in specific measurements to achieve certain results. Music deals in specific tones and tempos to achieve specific desired effects. Photography has specific light settings for specific desired results. Chemistry employs specific criteria when testing or doing comparative analysis etc - and they jot in down (X happens when you do why and z- specifically). When making soap detergent the combinations of ingredients are rarely random - if they want consistent results.
  Math equations are specific for whatever purposes they need to be, and computer software programs are specific to achieve desired results. Electronic circuitry has to be specific for the lights to go on - if i cut one wire, the power wont work properly. With electricity we can see how we affected the situation. An electrician can see specifically.
  I want to know specifically, what I did to my amino acid to change it.
Fledarmus - u can answer this; you said lemon juice is acidic enuf to "protonate the amine". Is that enuf to no longer make it valine. If i add salt, which is common in the prep process, will that further the issue of Valine no longer being Valine. This is the correct path of query that will help me. And the study can't include "pretty stable". In addition, when we say "burn them", what would be the temperature we speak of, specifically. 30C ? 100 C ?. Hair has proteins and amino acids and can burn easily (and be vaporised). Those vapors cannot perform as proteins and fold or exhibit stages (tertiary, Quaternary etc).
  I am very much interested in the "laboratory conditions". That is where the truth is, and conjecture and theory have to wait outside the room. In the lab is where so many criteria can be introduced to the amino acid and then studied to see "what happens" under the various conditions, specifically.
  I understand that many if not all on this forum are not in a lab testing these amino acids under various conditions and compiling data. Maybe no one out there is. I will continue to search for that person or persons who has done the specific studies and who has data, or who is willing to test the 9 essentials in various circumstances.
 

[discodermolide]

If you treat amino acids with an acid you will form a salt of that amino acid, it is still the amino acid it was (is) you have not fundamentally changed the chemical structure.
To change the chemical structure and make it no longer an amino acid you have to start breaking bonds. Breaking bonds can be achieved under a number of conditions, strong heating, strong oxidizing conditions, strong reduction media and so on. The compounds produced are no longer amino acids.
You must realize that amino acids are really quite stable compounds consequently harsh conditions are required to destroy them.

[Olivia james]

If harsh conditions are required (and we are still being general again), then how do these many, uber many, different changes and modifications and marriages etc occur on their own to form and change amino acids? If "harsh conditions" are required then how do all of these many multiples of changes occur to the amino acid inside the body.
  If amino acids are quite stable, how do they ever then change and modify and assimilate so easily into the matrix of digestion and other body processes?
 There is an inconsistency somewhere here and it is not my lack of deep knowledge. People work with amino acids all the time in labs etc and they are modified and changed and damaged all the time - under less than harsh conditions. If you're telling me that frying chicken or eggs or french fries in a vat of grease is harsh (i like to think it is) then okay, that's something I can wrap my mind around.
  Again, we are still being vague when we say "strong heating" or "strong oxidizing". This  tells me nothing as to what "strong" is. You are providing no reference, no scale. God and chemistry is in the details and this thread is truly lacking in the details. I can handle details people. I can handle a specific degree of heat or level of oxidation - i can't use generalities.
 I mentioned specifics in the last thread and i spoke of music and architecture etc. I forgot to including chemistry or at least pharmacology, which doesn't deal in "close enough". When creating drugs there are specific equations and portions of elements and compounds and molecules etc., that will do "specific" things when combined. Specific things to get a specific result. There is trial and error and all manner of experimentation, but still with specific variables/components and amounts of components etc.

[discodermolide]

If harsh conditions are required (and we are still being general again), then how do these many, uber many, different changes and modifications and marriages etc occur on their own to form and change amino acids? If "harsh conditions" are required then how do all of these many multiples of changes occur to the amino acid inside the body.
  If amino acids are quite stable, how do they ever then change and modify and assimilate so easily into the matrix of digestion and other body processes?
 There is an inconsistency somewhere here and it is not my lack of deep knowledge. People work with amino acids all the time in labs etc and they are modified and changed and damaged all the time - under less than harsh conditions. If you're telling me that frying chicken or eggs or french fries in a vat of grease is harsh (i like to think it is) then okay, that's something I can wrap my mind around.
  Again, we are still being vague when we say "strong heating" or "strong oxidizing". This  tells me nothing as to what "strong" is. You are providing no reference, no scale. God and chemistry is in the details and this thread is truly lacking in the details. I can handle details people. I can handle a specific degree of heat or level of oxidation - i can't use generalities.
 I mentioned specifics in the last thread and i spoke of music and architecture etc. I forgot to including chemistry or at least pharmacology, which doesn't deal in "close enough". When creating drugs there are specific equations and portions of elements and compounds and molecules etc., that will do "specific" things when combined. Specific things to get a specific result. There is trial and error and all manner of experimentation, but still with specific variables/components and amounts of components etc.

A strong oxidant is ozone a weak oxidant is dilute bleach, a strong reductant borane a weak reductant is hydrogen, strong heating is with a gas flame weak heating with a water bath.
These are chemical processes. In the body enzymatic (biochemical) processes take over. These conditions are of course much milder than those I mentioned, but just as effective.

[fledarmus]

These conditions don't occur "on their own" - they occur in the presence of a biochemical factory. Organisms have developed very selective catalytic systems in the forms of enzymes to carry out biotransformations that we attempt to imitate in labs using very harsh conditions that would never be found inside a body.

You are still confusing amino acids and proteins. Amino acids are building blocks of proteins. Each protein may contain between a few amino acids and thousands of amino acids. The body is pretty conservative in handling amino acids, but much freer with proteins. Proteins get produced and degraded on a very rapid timescale, but the amino acids are for the most part recovered and reused. Even cooking doesn't do much to most amino acids (with a few specific exceptions - google "chemistry of cooking" for pages on the exceptions).

So except for a few basic reactions on a few especially reactive amino acid sidechains, the amino acids themselves are not "changed and modified". They are assimilated - they are linked into huge protein chains, which are later digested to free up the amino acids to be reassembled into new proteins. When you ingest proteins, those proteins are also digested down to the free amino acid stage, the amino acids are transferred across the intestinal barriers, and then those amino acids are linked together to form new proteins.

As for what happens to amino acids outside the body and the biosyntheses of amino acids inside the body, these are the things that will take you at least two semesters of organic chemistry to get even the most basic information. It is simply impossible to tell you in any reasonable length of time every possible reaction that the 21 normal amino acids, or even the 9 "essential" amino acids can undergo, and what conditions are required to make them undergo those reactions. Like every other organic compound (and there are at least millions of different known organic compounds, if not billions), the reactions that it is possible for them to go are determined by the functional groups that are present. Find an advanced organic chemistry textbook and look up carboxylic acids - it will tell you the dozens of general reactions that carboxylic acids can undergo, and what conditions are required. Look up amines, and it will tell you the dozens of general reactions that amines can undergo, and what conditions are required. Look up alkanes, and you will find the (much more limited) set of reactions that the alkane portion of the amino acid can undergo.

If you have access to Scifinder or any other chemical reaction database, plug your selected amino acid into that. You should be able to get a listing of all the reported reactions that the amino acid has participated in. You're going to be there a while - I get over 4500 reactions for a preliminary search on one form of lysine as a starting material.

[Olivia james]

Life, the universe, is a bio chemical factory. That is what i meant by on their own. The human species was created - on it's own - in the perfect storm of various components, variables factors, etc. (hows that for generalizing).
  I am not confusing amino acids with proteins. the thread heading said death of an amino. I was not clear in my original post when i said "atmospheric forces". I later went on to clarify that I meant "outside the body" or in the kitchen say. The discussion of proteins came about somewhat inadvertently, and I thought i had steered the thread back to amino acids.
 I thought I also made it clear that i was not referring to the amino acids once inside the body, but rather before we ingest them - You missed that part and proceeded again to tell me about what happens inside the body with aminos acids.
  Strangely enough you are making my point about the amount of 'factors" that can impact change on an amino acid - When you say essentially, that you couldn't begin, online, to tell me "every possible reaction"  that can occur with aminos acids to alter or damage them, that is not in concert with "they are very stable".
  Your entire second to last paragraph is the reason for my inquiry; stuff does happen - on it's own. Things come together and break apart all the time in the natural world, forming new molecules or more of the same molecules ( or mutant molecules?).
 That sci finder database is a brilliant idea; with that I can begin to see what if any, conditions (criteria) exist that might be similar to cooking and food prep (or at least something that I, the lay person, can make sense of).
   Disco: You still spoke in generalities, albeit specific generalities - "How strong is joey?" - "he's strong like mike tyson or strong like bull" - 'Specific generalities' - I don't really know how strong mike tyson or a bull is.
  Here is what this dumb guy knows, generally speaking; All proteins and amino acids are different and require different criteria to create them and to "uncreate" them. But, they all can be uncreated. That is the nature of all things. Every life form has different factors that make them hardier or weaker than another. We have extremophiles that live in "harsh conditions" but they too have "breaking points". All things have breaking points, and because we don't know what particular factors will bring them to that point, that doesn't mean that there are not specific things that will destruct them. Therefore it is always best to do away with generalizing. Science and medicine aims to find specific causes and specific solutions - all based on at first and at times, non specific and random variables - til we hone in on those factors, those variables, that can prove in time to be part of a specific equation to address a specific issue.
  Among other things, when science and medicine become lazy and generalizes, we end up with all manner of disclaimers with the meds we ingest.

[fledarmus]

... I can begin to see what if any, conditions (criteria) exist that might be similar to cooking and food prep (or at least something that I, the lay person, can make sense of).
   

This is why it sounds like you are thinking about proteins and not amino acids. The conditions that you find in normal cooking and food prep, while they can have extremely varied and interesting effects on proteins, are simply not harsh enough to break down most amino acids. That is also why I say that amino acids are relatively stable - they are essentially unaffected by anything you would normally run across in day-to-day life. Take valine, one of your examples - it doesn't even melt until you get up to 600°F, and by then everything else in your food is burned. If you make a really fine dust of it, you can get it to ignite at somewhere over 700°F, and you can actually burn it in oxygen if you get it hot enough. It will actually decompose if you get it hot enough, but that temperature is well over 700°F. You can use bleach to form a chloramine and couple that to another amino acid, building up protein chains again, but you can digest it right back down to the amino acid. The easiest chemical reaction for an amino acid to undergo is coupling to another amino acid, and without the enzymatic machinery of the body, even that is difficult. Vinegar and lemon juice will do nothing.

But just because a compound is relatively stable doesn't mean we can't develop lots of reactions to carry out on it. Chemical labs use much more reactive compounds than those you will find in your kitchen. The measure "relatively stable" comes from the reactivity of the compound we have to put with it to get any reaction at all!

[Olivia james]

You are stuck on proteins - not me. I already know proteins can be impacted far easier than the components (the amino acids). But again, amino acids can and are impacted as well. In addition, they are not as impervious as you would have anyone believe. The sun's rays can impact amino acids and alter or damage them. The sun can also play a role in creating amino acids. Your skin and hair can be damaged irreparably by the sun. Your hair and skin, with all of it's amino acids, can be damaged beyond repair from temps as low as 180 degrees.
  Oxygen, can impact aminos. Light can impact aminos. Ph issues can more than any other factor, impact and corrupt an amino acid. Water or the removal of water can impact an amino. And none of these require harsh or extreme conditions. A salad has a lot of things going on with different levels of Ph from citrus fruits, and plants in the bowl and vinegar, salts, etc...
 Death, on it's own, can impact and degrade amino acids. All of the things we eat from plants and animals (with the exception of cookies), are dead entities, and are experiencing varying degrees/stages of decomposition - including the amino acids. If i find a dead mouse in my house and leave it there. It will decompose. Those amino acids will decompose as well - "on their own" (and by own their own I mean aided by other factors in the natural environment - and in the carcass). When the biodegrading process is complete whats left of my dead mouse is a pile of bones and some hair maybe. That hair and bones will have amino acids remaining perhaps, but the rest of the aminos that were in the rest of the body will have converted to gases (nitrogen etc).
  My point is most of what we are eating is already undergoing chemical changes. Each protein and amino is now already challenged and not as it is like when a lion eats a fresh kill. What most of us eat - the nutrients are already long since compromised.
   Aminos, "the building blocks", are impacted all the time and they in turn impact proteins which impact cells and cell tissue which can create rogue cells and hence disease etc. These dynamics are not extreme. the results can be, but the causes are ever so slight as the simple altering of one eency weency atom (or electron?). Of course I am now referring to what happens inside the body, but it is naive, or at least stubborn, to think that these complexities can't and don't occur in simple ordinary everyday circumstances.
  If you don't think that aminos get radically altered in your hamburger or anything in your barbecue pit then your're not really paying attention, or like me, you don't have access to any instruments of analysis. Again, the truth is in the actual analysis - electron microscopes, spectrometers etc. If you did a before and after analysis of a meat amino acid (steak) before and after the pit - you will see that the molecular makeup of even the hardiest amino acid will be radically altered. Until you've done that - this thread is all speculative, however smart you guys are.
  By cooking and prepping our foods we are dramatically altering our nutrients including amino acids- for the worse. We are not making them more bio available. The natural whole foods are already "bio available". No other species needs to have their nutrients be made more available to them. No other species damages their nutrients before ingesting them. We are the only species that combines so many food types with their respective chemical properties (salad) and we don't really know all of what is truly going on (without those special instruments of analysis).
 Make the connection to nutrient damage form a molecular perspective. Make the connection between nutrient deprivation and disease. Dispense with the lazy science and pat answers and generalities.
   It was Einstein who said "I have little patience with scientists who take a board of wood, look for it's thinnest part, and drill a great number of holes where drilling is easy".
 

[Olivia james]

Let me explain one mo gin, the difference between specificity and generalizing - or not getting what I am endeavoring to determine.
  You mentioned that Valine melts at roughly 6 or 7 hundred degrees F. That is for the whole of Valine. Specificity from my end looks at the bonds of atoms that make up the amino acid in the first place. Those bonds are broken before the overall melting is done or complete. At the point that the first bond is broken, the first of any of the atoms is removed,  from the "collective" if u will (the amino acid Valine), or side chains irreparably damaged, then the amino acid valine is no longer the amino acid valine. That was a premise established in this thread - and not by me (although i concur).
 So again, I am trying to determine at which point do these various bonds begin to break - before the final meltdown in the case of exposure to heat, rendering ashes of whatever. At that point, the first bond break, the amino is "dead" (inactive) and unable to do what it was biologically able to do - or at least do what Valine can do.
  This way of "testing" would be the same using Ph exposure or light and oxygen etc: At what point is the first bond in the amino acid breached.