Determination of the actual atomic arrangement in tartaric acid in motivated a change in stereochemical nomenclature from Fischer's genealogical. ethylenediamine ligands: a stereochemical primer . bones as planar, or having identical conformations. With this Greek letters λ and δ and correspond to left handed and right cobalt, these relationships are reversed. in bone, the individual fibrils are aligned head to tail, with a gap of 40nm between fibrils, STEREOCHEMISTRY OF AMINO ACIDS One of the interesting Just as our own left and right hands are (in principle) identical but different (in that .
If you want to be more environmentally friendly, you could think of a Prius, or something like that. So whatever your car is, oxygen is like the passenger for that car. And so hemoglobin goes by the lungs, picks up oxygen, delivers it to the tissues. And then tissues are just groups of cells that are of a similar type, and so each of the cells in these tissues then takes the oxygen and uses it to generate adenosine triphosphate, or ATP, which is the energy source for all the various metabolic processes that go on within our cells to help keep us alive.
So now where do amino acids fit into all of this? Well, amino acids are the building blocks of this hemoglobin protein.
And so without amino acids, this entire vitally important process wouldn't be able to occur. Now, sticking with the car analogy just a little bit longer, just like we have different types of components that come together to form different types of cars, whether it be a Porsche or a Prius, what have you, you can have different types of amino acids. And there are 20 of them-- to be exact-- that can come together to form countless, countless different types of proteins.
And so now that you have an idea of where amino acids fit in this bigger picture of a metabolic process, let's go ahead and take a closer look at what the actual structure of an amino acid is. First, we have the amino group.
And then we have the carboxylic acid group. And already you can start to see where the name amino acid comes from.
A2. Amino Acid Stereochemistry - Biology LibreTexts
You have amino, from the amino group, and then you have acid from this carboxylic acid group here. And then linking the two groups is this carbon atom, which we call the alpha carbon. And then bound to the alpha carbon is a hydrogen atom as well as a unique side chain, or R group. We just use R to denote any generic side chain. So each of the amino acids has this same generic structure, and what makes each of the 20 amino acids different from each other is this R group, or the side chain.
So each of the side chains for the amino acids is going to look different. One thing that's important to note is that this carbon atom, the alpha carbon, is also known as a chiral carbon. And what does a chiral carbon mean again?
Well, a chiral carbon is a carbon atom that has four unique groups bound to it. So if we take a look at this carbon, we can see that one group that's bound is the amino group. Another group is the carboxylic acid group. The hydrogen atom makes the third group, and then the fourth group bound to it is the R group or the side chain. And so the alpha carbon in amino acids is considered a chiral carbon. However, they do not all have the same configuration in the R,S system: L-cysteine is also R -cysteine, but all the other L-amino acids are Sbut this just reflects the human decision to give a sulphur atom higher priority than a carbon atom, and does not reflect a real difference in configuration.
A2. Amino Acid Stereochemistry
Worse problems can sometimes arise in substitution reactions: It follows that it is not just conservatism or failure to understand the R,S system that causes biochemists to continue with D and L: As mentioned, chemists also use D and L when they are appropriate to their needs.
The explanation given above of why the R,S system is little used in biochemistry is thus almost the exact opposite of reality. This system is actually the only practical way of unambiguously representing the stereochemistry of complicated molecules with several asymmetric centres, but it is inconvenient with regular series of molecules like amino acids and simple sugars.
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. 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.
Amino acid structure
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.
Amino Acid Dating. Is it reliable?
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 aroundmiles 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. 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 Both of these processes can potentially be used as a dating tool.
Let's look at both of them. 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 Abelson 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: Concerning the survivability of Biological Macromolecules and even spores, see: