Jens

The energy in the high energy bonds is measured by the energy (actually it is delta G) you obtain by splitting the molecule via the reaction with water precisely at the bond in question (This is called hydrolysis). In the hydrolysis reaction the high energy bond is not split into two (producing radicals), but it is moving from one atom of the original molecule to an atom of the water molecule.

Both sides of the bond are relevant for the energy. So if both sides are acids (e.g. Phosho-group on both sides like in ATP), the energy is higher than if one side is an acid (e.g. phospho group) and the other an alcohol group (-OH). There is a clear correlation between the energy of a bond and the acid strength (pK_a) of the two molecules you obtain after hydrolysis.

Try http:/scholar.google.com/

with "ic50 values of gallic acid" I got results (some only visible in the cache said 8.14 -- but you to verify )

thanks for your reply.

 

An expert said putting an apple(not peeled) in water for more than 15 minutes will lose xx% of its vitamin C , cuz it goes into water. (It is water soluble).

Is that true ? or crap ?

 

i often put apples in water with a little amount of salt in order to get rid of pesticide.

Sugar is also water soluble. If the apple does not taste sweet any more after 15 min, than the statement of this "expert" is true

But honestly: That's crap.

You will only loose Vitamin C, if you put the apple in a mixer, add water, mix it thoroughly, filter the suspension you obtain, do not drink the liquid part and eat the non-soluble part.

Here the structures to better understand why N-formyl-Met has the same structure as a peptide:

....by the way: These kind of questions (pointing out an apparent paradox) are exactly the interesting ones. Discussing potential answers help to increase true understanding....

Ammendment:

Giving the usual concentrations of vitamins in the pills, you do not need to worry about eating an overdose of a fat soluble vitamin (if you keep your consumption roughly at a usual level).

From a biochemical point of view:

Most vitamins are cofactors of enzymes. So having more of them as you need to construct those enzymes does not help.

However, this is different for the antioxidants (Vitamin C). They are active by themselves. A higher contration increases the probability that an agressive oxygen radical is reacting with them instead of reacting with something important in the cell (and destroying it).

Some input to your thoughts:

• Some fat soluble vitamines are actually toxic in overdose.
• Vitamin C is the main antioxidant. It is water soluble. The body can get rid of overdoses quite easily.
• Given the usual nutrition in wealthy countries it is actually very difficult (nearly impossible) to suffer from lack of vitamines.
• Of course there are a lot of companies who like making money be selling cheap chemicals at high prices.
• (At least in Germany) buying Vitamin C as pure chemical substance is much (often a factor 10 to 100 -- giving you an idea about the economic margin) cheaper than in form of vitamin pills.
• Just think you are the responsible head of marketing of a non-competitive (simply because it is more expensive in production) nutrition product. Would it not be fine to have a story around antioxidants, which is not even a lie? (Who of your customers would ever have a look at the quantities, or can estimate, if this is relevant at all, or can really compare it with other products, which even might have more antioxidants, but from a slightly different substance?)
• Humans (actually all primates) are one of the few animals for which vitamin C (the main antioxidant) is actually a vitamin. Means humans have lost the ability to synthesize ascorbate (= vitamin C). Most likely because our ancestors were fruit eaters, so they really did not need this capability. There are scientists claiming that the high concentration of uric acid in the human blood are intentionally regulated at this level (just below creating deseases), because it also acts as an antioxidant (but not as powerfull as vitamin C). So adding the daily rate of vitamin C (or twice that amount) in addition to what you normally eat certainly does not pose an issue and might actually help (some scientist think so, I also think so, but I am not sure).
• Vitamin C is sold as ascorbic acid. Acids are not too good for your teeth. So it is to be taken with the meals and definitely not in every drink you take between the meals (same thing with as with sugar).

My whole family had a viral conjunctivitis. It started with a bacterial conjunctivities of my father who visited an ophtalmo in vacation in rural France. After receiving antibiotics everything was o.k. again for some days. After 1 or two weeks (I do not remember any more) however it started again. Later the second one turned out to be a viral conjunctivitis (He got infected at the ophthalmo.)

It is really very infectious! You solely rely on your own immuno system. After 2 weeks your immuno system is gaining. After 3 weeks it was over.

We all were nevertheless treated with antibiotics (in form of eye drops). The reasoning was twofold:

a) The tests take some time and the phycians do not want to take the risk that an antibiotic resistent bacterium is irreversibly destroying parts of my eyes. So I even got treated by 3 different antibiotics sequentially.

b) It is quite common that the virus infection causes additional infections by bacteria.

Do you think it possible that natural selection can ever stop happening in a life form at some point? For example, let's say the DNA (or whatever) is not only the carrier of genetic information, but also serves as a physical structure of the organism that is critical for life. Then if the carrier of genetic information has mutations, it would affect the physical structure, thus resulting in death. And of course then no possibility of passing on the mutation. Or am I getting too far fetched?

What you are describing is exactly one part of darwinian evolution (the selection part). Since the mutations are random most of them have a negative impact and some of them might lead to death. This means those highly negative mutations (deadly mutations) are not passed to the next generation in contrast to neutral or benefitial ones.

1 from a chemical point of view all life is a reaction capable of self perpetuation, and change(dose not mean evolution, it means change in the literal sense)

2 from the human perspective all life is biological and needs to be capable of evolution

3 from a technological point of view life is a sufficiently complex system that is capable of creating new, more complex systems, or improving upon itself, increasing its complexity

4 from a philosophical point of view "i think, therefore i am" intelligence defines life

5 from a universal point of view, every system feeds into a larger system of infinite complexity (there is no real word to describe it, i guess something between "life" and "existence")

Interesting. I agree with respect that you can have different point of views on the definition of life, which are simultaneously rigth and wrong depending on the view. However, I will still try to defend my view

1: Agreed. If a system is capable of self perpetuation (or reproduction) and change, evolution will occur automatically.

2: Life is biological nearly only means life is life. Since biology is just the science of life, this does not state anything. Or you have the same issue in defining what is biological. So I do not think this definition is helpful.

3: Agreed. A computer system which is able to reach more complexity and even intelligence by adaption to some sort of input (most likely from the outside world), is probably considered at least as artificial life. The difference is that the complexity is not reached via physically reproducing the computer system to multiple with selection afterwards. However, there is still the question, if this complexity can only be reached via reproducing, mutation and selection of algorithms. If the answer is yes, than also Darwinian evolution takes place at the level of algorithms.

4: O.k. you can have this point of view. But it means that plants, microorganisms, fungi and most animals are not considered as life. So I rather vote for having intelligence and life as two different concepts like in common usage of the terms (outside science). So I also think this definition is not helpful (too far away from common sense usage of the term "life").

5: That's too abstract from my personal point of view to be helpful (especially the "infinite" part).

I will try to make an update on my definition based on your input within the next week (and post it here).

you could also say it it the carbon backbone.

all life is built using carbon chains as the backbone to the molecule, its just convenient, stable, and it can make alot of bonds.

 

carbon gives life structure

I agree.

For the environment of life it is liquid water, for life itself it is carbon with its capability of forming stable chains and other diverse chemical properties.

Some additional facts:

• There is a specific tRNA for N-formyl-methionine.
• N-formyl-methionine (fMet) is only used in Bacteria and not in Archaea (which are also prokaryotes).
• Archaea also have Shine-Dalgarno sequences to initiate translation.
• Blocking the amino-group by a formyl group prevents the charged tRNA for N-formyl-methionine (tRNA_f) to be used in elongation of the protein.
• In fMet the N is in an amid bond like in a peptide. Just with the difference that no amino acid is used but formic acid. The positive charge of the NH₃ group has disappeared and instead you have a planar amid containing a CO group as H-bond receptor. So this is quite a dramatic change.
• fMet-tRNA_f initially binds to the P-site of the ribosome.

Speculation:

Since fMet closely resembles a peptide, you might assume that the Bacteria ribosome can only accept tRNAs with peptide-like ligands in the P-Site (which seems to be completely logical, since the P-site always binds the peptide, that's why it is called like this.). This feature could be an additional security feature to prevent translocation before the peptide bond is formed and thereby preventing the production of proteins which are cut into two pieces.

Archaea seem to have found a different solution to the problem.

So the formyl-group might be the analogous thing as the primer RNA for DNA synthesis.

I agree it is water. Liquid water (which means the right temperature and a bit of pressure, too).

Hydrogen bonds are key to life in the respect that they allow for:

a) specific interactions (without chemical reactions) of already quite small molecules (like base pairing of two RNA segments)

b) separate between two phases in liquids (hydrophil and hydrophob) to form membranes.

Besides H₂O, there is only NH₃ and FH which at least theoretically can provide a liquid with hydrogen bond forming capabilities (It does not work with heavier atoms any more and alcohols will not form in sufficient quantity on any planet to form liquid alcohol seas.). F is too rare. Liquid NH₃ is might be too cold for effective biochemical reactions.

I think you cannot compare the values, since the o-NO₂ group (in contrast to the p-NO₂) is sterically too close to the hydrolized bond and therefore to the active center of the enzyme. So the difference might at least partially be caused by the different NO₂ group position and not by the sugar.

(by the way: Are you doing the test at the hot spring temperatures? If yes: Do you have checked that the nitrophenol-glucopyranosid is not just hydrolized even without the enzyme at that temperatures in your buffer already? ... it is a quite energy rich bond...)

Back to the original question (even if the thread is very old):

The usual substances you have in food do not have any pharmacological effect they are just the very same basic molecules all living beeings are made up and are not dangerous no matter in which combinations you take them. They do not act by regulating or blocking some activity in the body and therefore do not have any side effects. Since in addition at ususal temperature they do not undergo any chemical reactions, no toxic effects can happen.

However, the thing is different, if you eat something which has a pharmacological effect. As already mentioned in this thread plants produce a lot of substances to kill animals (especially insects or snails). Sometimes (actually not too rare) those substances do not kill humans but have a special effect (e.g. coffeine, nicotine). So if you drink coffee or tea you are actually drinking a natural insecticide. Very rarely it might happen that combining two of those substances is making the effect of one stronger or more dangerous. This is like incompatible drugs. But even with real strong drugs this happens only very rarely. So that there are two plants which have no effect alone but are toxic when eaten together, is more a theoretical case.

You can be sure that you could read it in all the biochemistry books, if there had been a scientific documented case.

P.S.: some of the insecticids produced by plants are toxic proteins which "are designed" to survive the acidic stomach and very resistant to digestion (proteases) by the stomach in order to kill the insect. However, if you cook them, those toxic proteins get unfolded (denatured) and loose there toxicitiy completely and the same time are now easy to digest.

In addition to what Derin has written:

You should distinguish between respiration and fermentation. Both respiration and fermentation can work with other substances than glucose (in different microorganisms). For simplicity I just consider glucose.

For aerobic respiration of glucose your equation is right:

Glucose + 6 O₂ -> 6 CO₂ + 6 H₂O + much Energy

Anaerobic respiration of glucose means that O₂ is replaced by another substance (which is used to oxidize glucose). For example nitrate:

Glucose + 12 NO₃^- -> 6 CO₂ + 6 H₂O + 12 NO₂^- + much Energy

All forms of respiration use the energy to create a pH gradient and electric charge gradient across a biomembran. Those gradients are then used to create ATP out of ADP. ATP is the usual energy unit in cells. Anaerobic respiration is not done by animals or plants (just by bacteria or archaea).

Fermentation (is always anaerobic) means re-arranging a molecule (like glucose) and gaining energy by this. This is much less energy than in respiration. ATP is made out of ADP directly not via gradients in membranes.

Glucose -> 2 Lactic acid + a bit of energy

Glucose --> 2 Ethanol + 2 CO₂ a bit of energy

a) Yes as mentioned already above calories (cal) is just a unit of measure. Joule (J) is another one. You can simply convert them by a factor. You can use this unit of measure for Energy (U), Enthalpy (H), Free Energy (F), and Free Enthalpy (G). So using calories does not necessarily say what you actually mean. U is standing for heat at a fix volume. H for heat at fix pressure. F and G consider also in addition an entropy term.

Terminology correction: It is "Gibbs Free Energy" and not "Free Enthalpy" (I was directly translating from German). And it is "Helmholtz Free Energy" and not "Free Energy" (the same issue).

An enzyme can consist of many polypeptides: This means, if you unfold it, you see multiple independent chains.

An enzyme can consist of multiple subunits: This is a functional breakdown and the structure in which it folds.

Both statements are completely independent from each other:

Two subunits (like to fix shapes) can be on the same polypeptide chain (= two fix shapes linked loosely via a flexible part of the same polypeptide chain).

One subunit (forming one fix shape with a certain function) can consist out of multiple polyppetide chains.

See references 32 and 26 in this publication for ribozymes creating amid bonds (which might help for the correspnding hydrolysis):

http://bartellab.wi.mit.edu/publication_reprints/Bartel_Trends99.pdf

Because it is highly hydrophilic RNA cannot form precise hydrophobic cavets besides plat ones to bind aromatic rings. So cleavage at hydrophobic amino acids (besides Phe) probably will not work.

Hi,

some points to consider with regards to 'food value':

a) Yes as mentioned already above calories (cal) is just a unit of measure. Joule (J) is another one. You can simply convert them by a factor. You can use this unit of measure for Energy (U), Enthalpy (H), Free Energy (F), and Free Enthalpy (G). So using calories does not necessarily say what you actually mean. U is standing for heat at a fix volume. H for heat at fix pressure. F and G consider also in addition an entropy term.

b) The value that matters from a biochemical point of view point of view is dG ("delta-G" the free Enthalpy or Gibbs Energy), since this value 0, if the reaction is in exact equilibrium. dG includes energy and entropy. This is biological relevant and not just a theoretical consideration. There are autotrophic microorganisms which cannot survive any more or have to change their energy metabolism completely dependent on the concentration of some anorganic substances in their environment they live from. However, the biochemical standard dG°' assumes 1 M concentration of the substances (besides water) and pH 7. 1 M is not very realistic in virtually all cases. But it is typically still better than taking dU.

c) Actually from biological point of view, the bigger issue is not the entropy, but the capability of the body to do something useful (e.g. synthesizing fat, or fueling your brain, or doing muscle work) with the 'food value'.

Example 1: Cholesterol: Even though it is very reduced and has very roughly the same dU or dG value as fat, the body is not able to make any energy out of it, since there is no pathway to produce NADH or FADH₂. You can only make bile acid out of it, which partially gets lost in the gut, since it is not 100% resorbed back again.

Example 2: Starch is a polymer of glucose and has more energy than the corresponding amount of glucose molecules. However, in the gut starch is simply hydrolized to glucose, which produces some heat but no energy form the body can use (no ATP). So there is no difference between the two with regards of useful energy.

Example 3: Cellulose has nearly the same energy than starch (it is just another way of assembling glucose into a polymer). However, you will die of hunger, if you eat cellulose (The body just cannot break it down to glucose units). So a statement that cellulose has about the same 'food value' than starch is a bit misleading.

So the real value for the body should better be measured in number of ATP (or equivalent) you can obtain out of it.

Check out this May 2003(?) article from the American Society for Microbiology:

http://forms.asm.org...x.asp?bid=16349

Bacteria became a distinctive domain when its first member developed a cell wall to protect itself against internally generated osmotic pressure

 

"Three attributes seem essential for life and evolution: a source of energy; a capacity for making specific, even if imprecise, informational macromolecules; and a capacity for replicating. Although other properties would be useful and valuable for success and gradually emerged, seemingly a strong, stress-resistant wall was not initially required. However, as metabolic capabilities grew, the primordial organism's cytoplasm likely became increasingly crowded with an assortment of biochemical ingredients and salts, leading to an ever-higher osmotic pressure and making that crowded cell's ability to withstand turgor pressure valuable, if not essential."

 

I currently have his 2001 book, Bacterial Growth & Form (cited in link above), checked out from a local library.

 

~

Thanks for the interesting link.

I agree to the statement you quoted.

My favorite book which focusses more on the even earlier stages of abiogenesis is RNA worlds. This collection is also available online (so its free):

http://cshperspectives.cshlp.org/site/misc/rna_worlds.xhtml

Hi CharonY,

Actually I think sometimes it is worth to distinguish catabolic from anabolic pathways (but not between degradation and energy pathways).

But not to make students crazy by asking it in a test.

I have already a few times seen artifical metabolic pathways in scientific literature which clearly look like laboratory artifacts by chaining single reactions together which are never active in a cell because they are not in the same compartiment or not active at the same time. (only to see a few years later somebody actually proving that this is not working like this in living plants / animals).

So beeing aware of the gradient between NAD and NADP helps in a way to be especially cautious if they are combined in the same pathway.

Of course metabolism is a network and there are no 100% design principles, since it is not designed.

And yes: Metabolism is a network.

Example:

As everybody in biosciences knows humans cannot synthesize the essential amino acids. However, the thing is much more interesting, if you look at the details: Actually if you go through all the synthesis pathways of the non-essential amino acids and remove all the enzymes which are anyhow already there, because they are needed for catabolism of the amino acids, you make a surprising (at least to me) finding: There is only one amino acid left. The only amino acid for which there are specific anabolic enzymes is Proline. Why did I personally found this interesting? Proline is extremely common in the protein collagen, which is the most common protein in animals and not needed in plants at all. So retaining (or gaining) the synthesis capability for Proline is especially important, since this is the only real issue, if you just eat plants. It is always amazing to see how optimized nature is. For all other non-essential amino acids you can say that humans can synthesize them just by chance.

Jens

Actually, I think this is a prime example of a nomenclature being arbitrary. For instance, Glycolysis could be seen as an energy pathways under this viewpoint (it generates ATP) but also as a simple catabolic pathways funneling carbon into the TCA cycle for other, anabolic processes.

Hi. I agree. This is exactly what I meant with that the terms are not mutually exclusive.

Personally, I do not like this nomenclature, since it produces artifical problems. I just wanted to help.

The TCA cycle is not directly involved in ATP production, yet it produces reduction equivalents, which are crucial for oxidative phosphorylation.

Hello CharonY. I know. This is why I have written "mostly via NADH".

I agree to all what has been said by jp555 above.

A more detailed biochemical view on it:

Darwinian evolution is not contraint to DNA (by the way: Darwin did not know about DNA). Actually the majority of scientists think it started with RNA. This is nearly the same kind of molecule but with the huge difference that RNA forms stable 3-dimensional shapes with precisely shaped deep surface structures. Why does this matter? This is the exact requirement to act as a catalysator for specific chemical reactions (and this is mainly meant with gaining new properties). To start darwinian evolution chemically you need a small system or one big molecule wich is able to copy itself (directly or indirectly via a cycle) and the same time beeing able to form precisely defined 3-dimensional shapes (to act as a catalysator). However, even this is not enough the starter system or molecule must also be able to change a bit (e.g. via copy errors) and those changes should in principle allow for arbitrary 3-D surface shapes (to have the potential to gain a huge variaty of catalytic features) but without loosing the same time the ability to copy itself. Once this level is reached the system or molecule will evolve into much more complex and perfectly adapted thing, which we could easily identify as life and distinguish from dead chemicals. This is of course not restricted to RNA or DNA based life forms at all.

So to my point of view: no life without the principles of Darwinian evolution: copy with mutation and selection. (at least as long as somebody comes up with another principle how a chemical system can gain more an more complexity and perfect adaption to the environment). Darwinian evolution is not something specifc to the Earth.

I think that you need an additional qualifier because it seems to me that, by your terms, the Universe itself could qualify as "life". By the Universe itself I mean the whole set of exstant physical reality.

 

So, I would add, at a minimum: "Life is a chemical system (in contrast to artificial life) as distinguished from the Universe as a whole."

Hi,

thanks for the note.

But I do not understand:

What do you mean: The universe is also a chemical system and reproducing itself?

Since I am not an expert in astronomy a few words on the universe reproducing itself would be helpful.

Theory:

Light absorption by a molecule means that one electron is in a hgiher energy orbital after the absorption. The higher the energy of of the light (increasing from red to UV) the higher the energy of the molecule after absorption. This high energy state can lead to chemical reactions which are otherwise not possible and end up in a different molecule which does not act as a vitamin anymore.

However, vitamins are a completly unrelated set of molecules, so the question if light really can destroy a vitamin molecule has to be answered per molecule.

Standard textbook knowledge is that folic acid can be destroyed by light.

For other vitamins I do not know (some/most of them are surely stable).

Research in wikipedia and google scholar might help....

Hi,

back to the original question.

I agree with the others it is somewhat arbitrary and might not make sense to differentiate. However if you still stick to differentiation I would try the following:

energy pathways: A pathway that finally leads to production of ATP out of ADP.

Examples:

- ATP production via light in purple bacteria

- most pathways in Eukarya which oxidize molecules to produce ATP (mostly via NADH)

detoxification pathways: A pathway that ensures removal of a molecule out of the cell without gaining energy out of it

degradation pathway: a pathway that makes smaller molecules out of bigger ones.

Examples:

- digestion in animals degrades nutrition without gaining energy, just for the purpose of producing the buidling block molecules which are than transported into the body.

- energy pathways of organisms that oxidize biomolecules (e.g. like fungis)

so the terms are not mutually exclusive.

Rule of thumb:

At least in Eukarya the usage of the NAD⁺/NADHsystemis a good hint for an energy pathway (a mainly catabolic pathway), while the usage of the NADP⁺/NADPH system is a good hint for an anabolic pathway. There is no miracle about it, this is simply to optimze reaction speed. The concentration of NAD⁺ is much higher than the concentration of NADH (a factor of 100 to 1000) and the concentration of NADP⁺ is lower than the concentration of NADPH (a factor of 0.1 to 0.01).

A NASA panel stated the following:

"Life is a self-sustaining chemical system capable of Darwinian evolution."

from: Joyce, GF (1994) Forward. In Origins of Life: The central concepts. (ed. D.W. Deamer et al.) pp. xi-xii. Jones & Bartlett, Boston.

Or in separate statements:

- Life is a chemical system (in contrast to artificial life)

- Life is able to reproduce itself (in contrast to most abiotic chemical systems)

- Life is able to undergo evolution to obtain new features (in contrast to crystals or simple chemical positive feedback loops)

From my point of view statement 2 and 3 are essential. Statement 1 is optional and depend on how you want the definition of life to be.

This definition includes viruses and excludes artificial computer life.

Prions are excluded, because they cannot undergo evolution to obtain new features (they behave more like crystals).

I think it is o.k. to include viruses because some of the biggest viruses look more like degenerated parasitic cells and it is a bit strange to say they are dead because they lost their ribosomes and are dependent on other life forms for it (but humans are also dependent on other life forms).

Note that having a cell membrane or beeing able to catalyze metabolism is not included in this definition.

This definition from my point of view also holds to define the border between abiogenesis and evolution (and not only to identify extraterrestrial life, which was most likely the main reason for this definition).