Now, let's look at some specific examples. One type of atom that does not normally react is Neon. (See the picture to the left.) It already has the correct number of electrons in it's outside electron layer so Neon does not react. Neon, along with Helium and Argon are known as non-reacting gasses because they do not need to react to be stable.
Other types of atoms such as Hydrogen, Carbon, and Oxygen do not have the correct number of electrons to be stable by itself. Instead they have to share electrons in molecules to get the correct number of electrons in their outside electron layer.
Since we only have to look at the atom that is in the center of the molecule to find out it's shape, we will concentrate only on Carbon and Oxygen. All the molecules illustrated on this page either have a Carbon or an Oxygen as the center atom. Carbon will especially be of interest since Carbon is the center atom for all the different Amino Acids.
Both Carbon and Oxygen have a deficiency. Neither C nor O have the proper number of electrons in their outside electron layer. Because of that, they are not stable by themselves. They must react with other atoms to get the proper number of electrons in the outside layer.
Oxygen is short 2 electrons. So it must form two covalent bonds to obtain 2 more electrons than it normally has by itself. The picture to the left will help you visually to see how covalent bonds can help increase the number of electrons that an atom can have.
Oxygen can either form two single bonds or one double bond. Water is a good example where Oxygen attaches to 2 different atoms, each by a single bond. Carbon dioxide is a good example where Oxygen attaches to just one molecule through a single double bond.
Either way, the Octet Rule is satisfied and the molecule is stable.
Carbon is short 4 electrons. It must form four covalent bonds in any combination of single and double bonds so that it ends up with 4 extra electrons.
Looking at the picture to the left (or above) we see that Carbon can be satisfied with either 4 single bonds or 2 double bonds. (A third alternative is that 1 double bond and 2 single bonds will also work.)
A double bond allows 4 electrons to be shared. 2 electrons from one atom and 2 electrons from the other atom. A double bond allows an atom to gain 2 more electrons through sharing.
Looking at the picture to the left (or above) we can see that Carbon usually shares all its electrons with other atoms. It does this because it has to double the number of electrons to get an octet. Oxygen on the other hand shares only two electrons with other atoms. The other 4 electrons it keeps for itself.
What Determines the Shape of a Molecule?
Now that we know about covalent bonds and how an atom achieves an octet, we only need one more fact to understand why molecules have specific shapes.
Here it is. All electrons are negatively charged. What do we know about like charges? They repel each other.
We can see the same exact thing happen with magnets. If we have two magnets and we try to push two like poles together (Either North with North or South with South), we see that they push each other away.
That is what the electrons do to each other. They try to get as far away from each other as possible.
Now remember, covalent bonds have two electrons. These two electrons because they are part of the same bond, are forced to be in the same area because they act as a single unit, a covalent bond.
So what happens is that each bond tries to get as far away from all the other bonds. They spread apart since they repel each other.
In the Water molecule pictured to the left (or above) we see that it has two pairs of unshared electrons. These behave very much like the electrons in covalent bonds. They stick together in pairs.
So whether electrons are shared or not they behave the same. They repel each other.
In the Carbon dioxide molecule, 4 electrons in each double bond are held together. Since Carbon dioxide has two double bonds, and since a double bond acts as a unit, the two double bonds try to get as far away from each other as possible. What they do is get on the opposite side of the central Carbon from each other. This molecule is straight!
Both Methane and Water have a similar shape. In both structures, we have 4 pairs of electrons trying to get as far away as possible from each other. So they go in all different directions. Water is a bent molecule because the unshared electrons force the two Hydrogens to come toward each other a little bit. This allows all the electrons to be more or less equally spaced apart.
Methane should be very interesting to us because it's structure is just like the Amino Acids that we are going to be looking at. All four Hydrogens are spread apart as far as they can be from each other.
The Structure of Amino Acids
Let's look at the central carbon of an Amino Acid. It is called the a Carbon. The a Carbon has the same distribution of electrons as we saw in Methane. The four bonds are spread apart as far as they can be from each other.
Often when we draw molecules on paper. We tend to think that the farthest the bonds can get is up, down, right, and left. However we must remember that molecules are not limited by 2 dimensions (like what we see on paper). Instead, the bonds spread out in all 3 dimensions of space. The angle from one covalent bond to another is 109.5o
This shape that the a Carbon bonds take is called a Tetrahedrial Shape. If we were to look at a 3 sided pyramid. (4 sides if you count the bottom) The a Carbon would be in the center and all the points (one pointing straight up, and the three others pointing toward the ground) would be sticking into the points of the pyramid.
In this structure, every covalent bond is angled 109.5o degrees from all the other covalent bonds. So, between every two bonds in this structure is an angle of 109.5o degrees. All the angles Equal each other.
Now we are ready to start looking at the structure of the Amino Acids.
An Amino Acid has a central a Carbon that has four groups attach to it. As you can see in the picture to the left (or above), the groups are: An Amino group, a Carboxyl group, a Hydrogen, and a side chain.
There are 20 different Amino Acids, In addition there are several other non-standard Amino Acids that are found in various peptides, polypeptides, and proteins. Each of these different Amino Acids have different side chains. So each Amino Acid has it's own specific structure, and the place where they are different, is the side chain. The side chain is what allows all the different Amino Acids to have their own specific characteristic.
The Amino and Carboxyl groups are also important because they are what allow Amino Acids to link together to form long chains forming peptides, polypeptides, and proteins. What happens is that the Amino group of one Amino Acid reacts with the Carboxyl group of another Amino Acid. This produces a peptide bond, which allows the two Amino Acids to be attached to each other. This process continues until long chains of Amino Acids can be produced. So the Amino and Carboxyl groups make up the backbone of protein chains.
In physiological condition, (meaning the conditions inside the body) a Amino Acids form what is called a "Zwitterion". What this means is that the structure of the Amino Acid has both a (+) positive charge and a (-) negative charge. We can see that the Amino group is (+) positively charged and the Carboxyl group is (-) negatively charged.
The side chains hang free and they cause proteins to have the characteristics that they have.
Most of the Amino Acids have a characteristic of shape that we need to understand. They are Chiral, meaning that they have a structure that cannot be superimposed on its mirror image.
We can look at our own body parts to know what this means. If we look at our hands and feet, we can see that they look somewhat identical except that they are backwards from each other. On our right foot, the big toe is on the left side, and on our left foot, the big toe is on the right. They are backwards from each other!
They are actually mirror images of each other which do not superimpose. But rather, they look different from each other. They are Nonsuperimposable mirror images.
It is easier to look at your hands. There is no way you can make your one hand look like your other hand. You either have your thumbs pointing in opposite directions or you are looking at opposite sides of the hand.
So both hands and feet are Chiral objects.
Other objects such as balls, glasses, and baseball bats (ignoring abnormalities such as the grain and name plate on the bat, etc.), we can always make these mirror images look like each other. The mirror images will superimpose. There is no such thing as a left-handed bat or a right-handed bat. They are all the same! So balls, glasses, and baseball bats do not have Chirality.
The a Carbon in most Amino Acids is also Chiral. A Chiral Carbon is a carbon atom that is bonded to four different groups.
The two Amino Acids on the left (or above) are mirror images of each other (just like our feet and hands). You can not make these two molecules look like each other. You can turn the molecule on the right around so that the H is on the right side and the NH3+ group is on the left but they still will not look like each other. The H and NH3+ groups will be going away from you instead of going toward you the way it is pictured on the left molecule.
The right and left form of amino acids are Isomers meaning that the two molecules have the same molecular formulas but different structures. In other words, the two molecules have the same atoms, but they only have them arranged differently. Any two molecules that have the same atoms are isomers. They do not even have to look like each other, they only have to have the same number of all the same atoms.
However, Amino Acids not only form isomers; The right and left form of Amino Acids are actually mirror images of each other. This fact makes them Enantiomers, which means they are two molecules that are nonsuperimposable mirror images of each other.
These same amino acids are also Stereoisomers which means that the two molecules differ in their three-dimensional shapes only but that they have the same structural formulas. This means they have the same exact groups attached in the same way. Only the three-dimensional orientation of these groups are different.
So, 19 of the 20 Amino Acids form isomers that are are both Enantiomers and Stereoisomers because their functional groups only differ in their three-dimensional orientation in such a way that they form nonsuperimposable mirror images of each other.
The a Carbon in 19 out of the 20 amino acids is a Chiral Carbon. Hence, 19 out of the 20 amino acids are Enantiomers (mirror images of each other). Partly because of this Stereochemistry, these molecules have become important to the Amino Acid dating process.
For the moment, let's look at the Amino Acid that does not have a Chiral carbon in it. It is Glycine. The reason why Glycine does not have a chiral center is because it has two Hydrogens attached to it. (The side chain is also a Carbon.)
Remember the definition of a Chiral Carbon was that four different groups had to be attached to it. Every one of the four groups has to be different, in order for it to be chiral. In Glycine, only three types of groups are attached to the central a Carbon. Just like the balls, bats and glasses, we can always make one molecule look like the other one. So Glycine does not form Stereoisomers.
In all of the other 19 amino acids, bonds must actually be broken and the molecules be put back together before the two molecules can look like each other.
This breaking apart of the molecule and putting it back together is exactly what has happened to the amino acids in the fossils. So of course this is the basis that some scientists use amino acids for, in seeing how long fossils have been in the ground. It is assumed that the rate that the amino acids have changed has been constant enough for it to be used as a dating process.
How does a Scientist tell the difference between different Stereoisomers?
This is an interesting problem. A scientist has to be able to distinguish the different Stereoisomers from each other. How does he do it?
We can easily tell the difference between left and right hands and feet just by looking at them. Hands and feet are chiral just like the amino acids we want to look at. However left (L) and right (D) forms of amino acids can be extremely hard to distinguish if we look at the wrong feature.
Stereoisomers, the left (L) and right (D) handed forms of amino acids, have essentially the same structures. They have the same exact chemical structures except that they are mirror images of each other. So they also have both the same exact physical and chemical characteristics!
They will boil and freeze etc. at the very same temperatures, they will react in the same way with other molecules. They do everything the same, except for one thing.
Actually there are at least two ways that left (L) and right (D) handed forms of amino acids can be distinguished. One is by reaction where an enzyme controls the reaction. Enzymes uses the shape of molecules to speed up its reaction. This by the way is why virtually all the amino acids in animals are in the left (L) handed form. Enzymes only incorporate and produce the (L) form.
Also, Enzymes will only react with amino acids that are left (L) handed. We can see how this works with a simple handshake. When we shake hands each of us hold out our right hands and the two hands fit into each other. They fit perfectly and we shake hands. If I were to take my left hand and try to shake his right hand, my fingers would be going in the wrong direction. The two hands would clash and not fit into each other at all. It just doesn't work. Even if I were to turn my left hand around so that it is upside down, I would find that now my fingers go in the right direction but my thumb would till be in the wrong place to match the other hand. The two hands would not fit properly. A handshake only works when both individuals use their right hands, or when both individuals use their left hand. In Biological systems, the same is true. Only when all the amino acids are left (L) handed, will the different enzymes and amino acids fit into each other.
Now, the other way that we can distinguish between left (L) and right (D) handed amino acids is that they rotate light in opposite directions. A way to measure the rotation of light is to use polarized light.
To understand what polarized light is, why don't you try an experiment. The next time you are in a department store, or some other store that has glasses, go to where they are and find the polaroid glasses. Pick two of them up and putting one pair of glasses in front of the other, view through two lenses at once, just like the picture to the left (or above).
You will find that when you rotate one of the lenses that the view through the glasses will go dark. You rotate the glasses back and then you can see through the lenses again.
Actually, to make this experiment easier, you can put one pair on your head, then view through the other pair. Rotate it and see what happens.
This is real neat but how does it work? Well we need to look at the nature of light to understand polarized light.
Light is a form of electromagnetic radiation, just like Radio waves, television waves, radar, microwaves, infrared waves, X-rays, and Gamma rays. A distinctive feature of electromagnetic radiation is that the velocity is always the same. The light goes at the speed of light, which in a vacuum, is around 186,000 miles per second.
Another characteristic of Light is that light is broken up into discreet units. They are actually bundles of energy which we call photons. Just like in a stream of water, it is actually water molecules (H2O) which are moving down the river. In a beam of light, it is actually photons of light which are moving along at the speed of light.
Light, like all electromagnetic radiation, exhibit the properties of wavelength and frequency. So we know that light acts like a wave.
For simplicity sake, let's describe a wave as a force that makes photons vibrate sideways. Looking at the picture to the left (or above) we see what looks like a wave. A photon of light is traveling from left to right. (We can see the arrow on the right so we know that the photon is going right.)
Now remember, we are keeping things simple. As light goes from left to right it actually follows the wavy line that goes up and down as it goes toward the right. So we can see that the photon of light can vibrate up and down as it goes toward the right.
Now each photon is independent from the other photons. So we could have some photons vibrate up and down, others vibrate in other directions. That is exactly what happens. Each photon vibrates in it's own plane, or it's own direction.
What a polaroid lens does is to let through the light that vibrates only in the proper direction. The picture to the left (or above) shows the first lens (in both Experiment 1 &2), as only letting through the light that vibrates up and down. All the other light is stopped.
Now, it's what we do with the second lens that determine the outcome of the experiment. If we have the second lens oriented in the same direction as the first lens, (as in Experiment 1) then only the light that vibrates up and down will pass through both lenses.
If on the other hand, the second lens is oriented as in Experiment 2, (letting only the light that vibrates right and left) then no light will reach your eyes.
Scientists use a Polarimeter to detect stereoisomers. If you look at the picture to the left (or above) you can see that a Polarimeter is very similar to our department store experiment. Except that an additional tube (a Polarimeter Tube) is added. The polarimeter tube contains a solution of a stereoisomer substance such as an amino acid.
Once the light goes through the first polarizer lens (just like a polarid lens) only the light that vibrates up and down get through. Now the light enters the tube that is filled with the amino acid. When it goes through the solution, the light begins to twist. The plane of light changes so that after the light comes out of the tube, it is now vibrating in another direction, not up and down, but a different direction.
It is the job of the second polarizer lens to determine how much the light has twisted or rotated. This second polarizer is rotated by the scientist until the light disappears. Then the angle is noted and recorded. So a Polarimeter actually measures how much the light has been rotated by a specific substance.
To test another substance, the scientist can replace one tube with another tube that contains a different substance.
Amino Acid Dating
Now, lets use this knowledge of chirality, stereoisomers, and left (L) and right (D) forms to help us understand how amino acids can be used as a dating mechanism. When the fossil was first buried in the ground, two different things start happening to the amino acids in the protein.
- Amino acids are unstable and they start decomposing with time.
- Most amino acids have at least one chiral carbon, hence, they have a left-handed (L) form and right-handed (D) form. With time, the amino acids undergo a process called racemization, where all the left-handed amino acids found in proteins change to a 50:50 mixture of (D) and (L) forms.
Both of these processes can potentially be used as a dating tool. Let's look at both of them.
Using the Stability of Amino Acids as a Dating Tool.
Some amino acids are more stable than other amino acids. So what happens is that as a fossil gets older, only the more stable amino acids are found in the fossil. So determining which of the amino acids are still in the fossil can be used as a dating tool.
The break down of amino acids occur at predictable rates. So that means that the rate of decomposing amino acids can be used as a dating tool. This was seen as far back as 1955 (Abelson 1955).
However, there are two problems with using this in dating fossils:
- There is a lot of variation in the numbers of amino acids found in living organisms. It might be that some of the fossils, when they were alive, had ratios that were more like the surviving amino acids that are known to be more stable. So because we are unable to know what the original ratios of amino acids were when the fossils were alive, it would be extremely hard to use the degradation process as a dating tool.
- Amino acids are expected to survive only a few million years at best. So detectable levels of most of the amino acids we see in fossils should not be present, if the long ages of Evolution are assumed.
This is the enigma I spoke earlier concerning the surviving amino acids in fossils. For a more complete discussion, see: the presence of amino acids in fossils. Concerning the survivability of Biological Macromolecules and even spores, see: the presence of DNA and bacterial spores in fossils.
Using the Racemization Rate of Amino Acids as a Dating Tool.
All of the 20 amino acids except glycine has a chiral carbon. As was mentioned before, these molecules can be found in either a (L) left handed form, or a (D) right handed form.
Unlike the above degradation process, we know what the forms of all the amino acids were in the living fossil, and we know what change will occur when the fossil gets old.
In living organisms, all amino acids are found in the (L) left handed form only. (There are some rare exceptions, for example, in the cell walls of bacteria, D-alanine is used so that the normal enzymes of most attacking predators will not be able to break down the bacterial wall.)
After the death of an organism, as when a fossil is buried, the population of (L) left handed amino acids start changing so that eventually, a 50:50 mix of both (L) left handed and (D) right handed amino acids will exist in the fossil.
The random process that produces this change is called Racemization. Without describing the intramolecular shift of hydrogen atoms that allow it to happen, we can simply say that the amino acid molecules slowly shift from (L) to (D) forms and then back to (L) forms in a random process.
The Racemization process is very much a random process and is somewhat like the random processes that involve radioactive isotopes for dating.
Initially, at the time of death, the reaction strongly goes to the right producing the (D) form quite rapidly, as is indicated in the first reaction in the graphic above. The graph to the left also shows that the loss of (L) form and the formation of (D) form is the most rapid in the initial stage at the time of burial.
As the concentration of the (L) form decreases and the concentration of the (D) form increases, equilibrium is approached. As equilibrium approaches, the net increase in the concentration of the (D) form from the (L) form decreases.
When Equilibrium is actually reached, then there is now no net change. The forward Racemization reaction is running at the same rate as the reverse Racemization reaction.
So it seems, at least on the surface, that the racemization of amino acids can be a very predictable process, and that it can be used as a dating tool because it is so predictable.
Unfortunately, this is not the case. Unlike radioactivity, which is extremely predictable, there are a lot of factors that can affect the rate that amino acids transform from one form to another.
Factors that affect the Racemization Rate
The following factors have been found to affect the speed of the reactions that causes amino acids to undergo racemization.
- Water concentration in the environment
- pH (acid/base measurement) in the environment
- Bound state versus free state
- Size of the macromolecule, if in a bound state
- Specific location in the macromolecule, if in a bound state
- Contact with clay surfaces (Catalytic effect)
- Presence of aldehydes, particularly when associated with metal ions
- Concentration of buffer compounds
- Ionic strength of the environment
The first three factors: Temperature, water concentration, and pH especially affect racemization. But, temperature is the factor which dramatically affect this process. If the temperature goes up 1o than the rate of racemization increases by 25%!
So it is acknowledged that if this process is to be used as a dating tool at all, it must be calibrated so that it's answers can agree with other dating tools such as Carbon 14.
What scientists try to do is to save money by using amino acid data on various fossils that they think have had similar characteristics and which have had experienced similar conditions such as temperature. They think that relative ages can be obtained through this method. This might be possible if the assumptions that they have made are correct; However, let's look at the data a little closer. It may be that the data would fit just as well, or even better when considering a short age synario. Let's see how probable it is that they are getting the answers they think they are getting with amino acid dating.
Racemization Rate vrs. Assumed Age
Let's look at the graph below. If Amino Acid dating was a predictable process, like other dating techniques with a predictable rate, the points on the chart would align themselves in a horizontal line. That would indicate that the Racemization constant really is a constant. It would mean that this method would be able to predict an age by itself. It would indicated that the rate would be the same rate for all the samples collected.
This is definitely not the case. Looking at the graph we can see that the Racemization constant changes almost as much as the predicted date!
What is really amazing to see is that the rate of racemization changes almost as much as the age, yet it is used as a dating method! It almost looks like the racemization rate could be independent of the assumed ages of the fossils. Maybe what is being measured is a difference in some of the factors which especially affect racemization. Namely: temperature, water concentration, and pH.
Because the rate of the racemization constant changes almost the same degree that the assumed ages of the specimens changes, the possibility must exist that the assumed ages are totally fictitious. In fact, if the assumed ages are tossed out and a approximate date for the occurrence of Noah's global flood is inserted; The graph would indeed approach a horizontal line. The very same result that is shared by other predictable dating techniques.
Another interesting issue concerning the racemization rate of amino acids is the assumption that amino acids within the matrix of a protein would tend to have a slower rate of change versus. other amino acids which are in a free condition, away from the interior of a protein. In the chart, some difference is detectable, however it is an insignificant difference when comparing all the other specimens. The chart shows that whether free or incorporated within a protein, the racemization rate of amino acids is more or less the same.
I would be dubious of any kind of amino acid racemization data because the racemization constant must be adjusted to give the answer that the researchers are looking for. Since amino acid dates are usually adjusted to match the dates of, say Carbon 14, the results are that of Carbon 14 dating and not amino acid dating. It should be clear that amino acid dating poses absolutely no threat to the Creation paradigm.
The insignificant differences found between free and non-free amino acids help bring into question the explainations used to explain why amino acids have not broken down. Have a look at my two pages on these issues. One is on the presence of amino acids in fossils, the other on the presence of DNA and bacterial spores in fossils.
Limitations of the Historical Sciences
In any kind of a historical science, assumptions have to be made in the assessing of historical dates. Because it is assumed that man, for example, has ascended over a long period of time, researchers would automatically want to lengthen the amount of time indicated by the artifacts uncovered in archeological digs. They are looking for answers that would fit their present model. I am not trying to say that they are falsifying their data. On the contrary they wouldn't need to falsify anything. Historical data can be so inconclusive that a host of positions is possible from almost any set of data that is collected.
Man is thought to have progressed through a long period of prehistory (cave man's experience) before some sort of civilization is started. Only after civilization begins can we begin to gather some sort of data from the discovery of the artifacts that are found (Pieces of pottery, etc.). The artifacts according to today's traditional thinking should be slowly progressing in complexity as it is thought that man is progressing in his abilities and ideas that he uses.
If man is thought to have progressed over long periods of time, even within the later civilization phase of his existence, than surely as the artifacts are recovered from archaeological sites, the theories and ideas developed will reflect the scientist's own original thinking. This is how science normally works. They normally work within fairly well defined set of theories that have become a paradigm. A paradigm is a theory that is so well accepted that no one seriously questions it. This way of doing science is most prominent when the evidence is fragmentary at best.
Assumptions throughout the scientific process are extremely important because they must hold the facts together. Only when specific data comes that either substantiates or falsifies the previously held assumption, can it be known if the thinking was originally correct. Unfortunately, with fragmentary data, the artifact that might falsify a theory is extremely hard in coming or it could easily be overlooked. So the problem must be solved by a host of assumptions that will probably never be tested.
There is also the danger that good data could be thrown out because it doesn't fit with established thinking. For instance, I am told that there are sometimes found in the same level both "early" forms and "modern" forms of man. Because of what is considered to be an impossibility, the modern forms are assumed to have been examples of intrusions. The modern form is considered to have been buried much later in spite of the fact that the specimens are found in the same level.
The areas of science, which are the most successful, which the public notices, are the amazing discoveries in medicine, biology, space exploration, and the like. These are the areas that deal with the here and now. If an experiment is conducted and the information needed to answer the problem is not forthcoming, then another experiment can be designed to answer the problem. The process can continue until some answer to the problem is
understood. The problem is only limited by money, ingenuity, and the technical difficulties that have to be surmounted.
In addition to the above limitations of science, historical science is limited by the fragmentary nature of the artifacts it is able to find. In effect, the accuracy of ideas
is limited by the assumptions chosen by the researchers.
Hopefully you will start to see this page start to grow. Sorry for the delay.
Some Interesting Papers
Amino acid racemization and the preservation of ancient DNA. Poinar HN, Hoss M, Bada JL, Paabo S
Science 1996 May 10;272(5263):864-6
University of Munich, Germany.
The extent of racemization of aspartic acid, alanine, and leucine provides criteria for assessing whether ancient tissue samples contain endogenous DNA. In samples in which the D/L ratio of aspartic acid exceeds 0.08, ancient DNA sequences could not be retrieved. Paleontological finds from which DNA sequences purportedly millions of years old have been reported show extensive racemization, and the amino acids present are mainly contaminates. An exception is the amino acids in some insects preserved in amber.
Predicting protein decomposition: the case of aspartic-acid racemization kinetics. Review
Collins MJ, Waite ER, van Duin AC
Philos Trans R Soc Lond B Biol Sci 1999 Jan 29;354(1379):51-64
Fossil Fuels and Environmental Geochemistry (Postgraduate Institute), NRG, University of Newcastle-upon-Tyne, UK. firstname.lastname@example.org
The increase in proportion of the non-biological (D-) isomer of aspartic acid (Asp) relative to the L-isomer has been widely used in archaeology and geochemistry as a tool for dating. the method has proved controversial, particularly when used for bones. The non-linear kinetics of Asp racemization have prompted a number of suggestions as to the underlying mechanism(s) and have led to the use of mathematical transformations which linearize the increase in D-Asp
with respect to time. Using one example, a suggestion that the initial rapid phase of Asp racemization is due to a contribution from asparagine (Asn), we demonstrate how a simple model of the degradation and racemization of Asn can be used to predict the observed kinetics. A more complex model of peptide bound Asx (Asn + Asp) racemization,which occurs via the formation of a cyclic succinimide (Asu), can be used to correctly predict Asx racemization kinetics in proteins at high temperatures (95-140 degrees C). The model fails to predict racemization kinetics in dentine collagen at 37 degrees C. The reason for this is that Asu formation is highly conformation dependent and is predicted to occur extremely slowly in triple helical collagen. As conformation strongly influences the rate of Asu formation and hence Asx
racemization, the use of extrapolation from high temperatures to estimate racemization kinetics of Asx in proteins below their denaturation temperature is called into question. In the case of archaeological bone, we argue that the D:L ratio of Asx reflects the proportion of non-helical to helical collagen, overlain by the effects of leaching of more soluble (and conformationally unconstrained) peptides. Thus, racemization kinetics in bone are potentially unpredictable, and the proposed use of Asx racemization to estimate the extent of DNA depurination in archaeological bones is challenged.
The kinetics of diastereomeric amino acids with o-phthaldialdehyde.
Meyer MW, Meyer VR, Ramseyer S
Chirality 1991;3(6):471-5 PMID: 1812958, UI: 92256092
Institute of Organic Chemistry, University of Bern, Switzerland.
The kinetics of the reaction of the amino acid epimers L-isoleucine, D-allo-isoleucine, L-threonine, and D-allo-threoninewith o-phthaldialdehyde and mercaptoethanol were determined at 25 degrees C. L-Isoleucine reacts faster than its D-epimer whereas L-threonine reacts slightly slower than its D-epimer. In the case of isoleucine, the consequence can be an allo/iso ratio which in the worst case is 25% too low if these amino acids are quantified by liquid chromatographyand o-phthaldialdehyde fluorescence detection. The effect on dating of fossils by amino acid racemization is discussed.