Wednesday, September 18, 2013

It’s Not Just Our Tooth That’s Sweet

Biology concepts – homochirality, carbohydrates, chiral discrimination, glycoside, H antigen


It isn’t just biomolecules that show chirality. There is also
chiromorphology, like snail shells that usually turn to the right
(dextral, or D-). There are factors in early embryonic
development that cause the body and shell to be right handed
in most gastropod species, yet other species are left handed.
There are also instances where a right-handed species will
produce a left-handed individual, so shell collectors have to be
on the look out for abnormal individuals.
A couple of weeks ago we talked about how, in most cases, life uses exclusively the left-handed enantiomers of amino acids to make proteins.  This homochirality is also see in the sugars we talked about last week, but in this case, mostly D-sugars are utilized in biological systems.

What isn’t amazing is that it happens to be L- for amino acids and D- for carbohydrates; the fact that they’re different is no big deal. Evolution just wants the parts to fit together, so if an enzyme evolved to use D-sugars, it’s not a surprise that the D-sugar would be favored in the pathway then now on. 

But it might not have been random either. No one knows for sure, but hypotheses abound for how homochirality in these biomolecular monomers was established.

One 2009 paper was concerned with the maintenance of homochirality rather than its establishment. Dr. Soren Toxvaerd stated that if you don’t believe life as we see it today occurred in a singular event, then it must have developed over a long period of time. Evidence indicates that small changes in the self-assembly of biomolecules took place over at least thousands of years.

If life took a long time to develop, then prebiotic (before life) earth must have been fairly stable in terms of enantiomer concentrations. But we know that homochiral solutions will turn to racemic mixtures (containing both L- and D- enantiomers) in a short time, days for amino acids and just hours for sugars. So how could the environment have been stable enough for life to develop over time?


One possible hypothesis about the establishment of homochirality
was put forth in 2010 by Koji Tamura, PhD in the Journal of
Cosmology. Put very simply, RNA may have developed before
proteins. RNA evolved to use only D-ribose because a mixture
would have been a symmetry violation. The action of D-ribose
would have been driven toward L-amino acids because of shape
problems with attaching D-amino acids to tRNAs. Now prove it.
Louis Pasteur, he of bacteria-free milk and germ theory, may have shown us the way. He discovered chiral discrimination. Racemic mixtures, under the right conditions, will separate into pools of homochirality. There is an energy gain and stability to packing homochiral molecules together; the other enantiomer will be excluded. This could help explain life using one enantiomer only.

What is more, hydrothermal vents and black smokers have just the needed conditions for both chiral discrimination and for self-assembly of biomolecules. Interesting huh? Think it’s a coincidence that black smokers harbor some of the oldest archaea on Earth? We may owe our very existence to plumes of superheated water and the xenophobia of enantiomers.

Lastly in this area, it may be that sugars and amino acids selected each other for homochirality. Glyceraldehyde is 1) highly discriminate for its enantiomers, 2) was present in large amounts in prebiotic oceans, 3) is used in self-assembly of many biomolecules, and 4) D-glyceraldehyde very much likes to bind to L-serine. So a slight excess in either one of these could have helped select for the other, and if this was stable, it could have caught on like “Gangnam Style.” This may be why life uses mostly D-sugars and L-amino acids and why I know the name Psy.

Now that we have delved into the mire that is maintenance of homochirality in sugars, let’s look at the rule breakers. D-sugars aren’t the only game in town.

Bacteria, oh bacteria! Once again, they lead the way in rule breaking. Last week we discussed how E.coli can generate ATP from several different sugars - glucose, lactose, etc. It takes different enzymes to metabolize each sugar, so if they are going to invest the energy in maintaining those genes and making those enzymes, there better be a good reason.


Paracoccus species 43P  has been shown to have an L-glucose
metabolic pathway. This organisms is very closely related to
Paracoccus denitrificans. P. denitrificans is believed to be the
organism that was engulfed to become the eukaryotic
mitochondrion. It closely resembles the mitochondrion, and
although random genes needed for aerobic respiration have
been found in many prokaryotes, P. denitrificans is the only
prokaryote in which all the necessary genes have been found.
A 2012 study tried growing soil bacteria on medium that contained only L-glucose as an energy source. One species of bacterium, Paracoccus sp. 43P, was able to metabolize L-glucose to pyruvate and glyceraldehyde-3-P, and then make use that for ATP production. The researchers discovered an L-glucose-specific dehydrogenase enzyme, and this enzyme was active in the fluids from broken up paracoccus cells. The process is similar to one in E. coli, but here it is L-glucose specific.

Mammals can’t manage as well as some bacteria; we can’t metabolize L-glucose at all. However, that doesn’t mean it can't work for us. L-glucose has been proposed as an artificial sweetener, especially for type II diabetics. One form of L-glucose can stimulate insulin release, so this would be doubly good for type II diabetics. Unfortunately, L-glucose costs 50% more than gold; therefore, don't look for it next to the Truvia anytime soon.

One, but only one, study has been published showing rats metabolized L-fructose and L-gulose, but not L-glucose. From 1995, the authors waited until the end of the paper to explain that the metabolism was being carried out by the rodents gut bacteria, not by the rats themselves. No wonder it was only one paper.

Just because we can’t metabolize L-sugars doesn’t mean that we mammals are left out in the cold. Some sugars are used in the L-form even if they aren’t broken down to make ATP. The most egregious example of this is a hexose sugar called L-altrose. Why is it different than some other exceptions here? Because altrose doesn’t even occur in nature as a D-sugar; only the L-form has ever been found. It was first isolated in 1987 from a bacterium called, Butyrvibrio fibrisolvens, which is found in the GI tract of ruminate animals (cows and such).


Ruminants are mammals that have more involved digestive
strategies. Ruminants have many types of GI bacteria to help
them break down tough plant material; it isn’t surprising that
some of them can use nonstandard carbohydrates in their
physiology.  “Ruminating” is the act of re-chewing food that
has been partially softened by bacterial action in the first
compartment of the stomach, and then brought back to the
mouth as “cud.” I ruminate on ideas all the time, but I think I
will stop – I’m going to call it “further thought” from now on.
Ruminates go the extra mile. They digest longer and work on food harder, using bacteria to help with much of the work. Therefore, it isn’t strange to note that L-altrose has also been seen in another ruminate bacterium, Yersinia enterolitica. Remember though, this altrose isn’t being used in energy production; it's found in their outer cell wall glycoprotein, LPS (lipopolysaccharide).

It turns out that L-sugars are common in bacterial LPS. I found examples from several different bugs, including L-quinvose (6-deoxy-L- glucose), L-rhamnose, and L-fucose (6-deoxy–L- galactose).

When it comes to L-sugars, plants can get into the act as well. Rhamnose  (6-deoxy-L-mannose) occurs in nature, and can be isolated from several plants of the genera Rhamnus and Uncaria, including Buckthorn, poison sumac, and many other plants.

Rhamnose from plants takes the form of a glycoside. There’s there word again, glyco-. A glycoside in general terms is any molecule bound to a sugar. In plants, attaching sugars to create glycosides is a common way to inactivate molecules so that they can be stored for later use. When needed, the sugar residues of glycosides are cleaved away by special enzymes and then the protein, enzyme, lipid, etc. becomes active.


Digoxin (or sometimes digitalis) are cardiac glycosides from
foxglove plants. They are used to treat atrial rhythm or heart
failure problems. First used by William Withering in 1785,
digitalis is said to be the first of the modern day therapeutics.
But it can kill you too, both the plants and the drugs. A nurse
was sentenced to 18 life sentences after he was convicted of
killing more than 40 patients with digoxin.
Glycosides can be differentially regulated because there are many sugars that can be used, and several different possible linkages for each sugar/substrate combination. Therefore, cells can precisely control just when and where the glycosides are activated. This may allow cells to function for longer periods of time, but isn’t the reason that rhamnose and fucose (both L-sugars) are being included in obscenely expensive anti-aging creams.

Some evidence suggests that rhmanose and fucose can inhibit the activation of the elastase enzyme in skin cells. Elastase is known to increase in expression and activity as skin cells in culture divide several times. Therefore, companies want you to believe that rhamnose will keep your skin from looking old. Forget that keratinocytes in a petri dish bear as much resemblance to your skin as Watchmen does to Hamlet.

That was a bit sarcastic, but the cosmetic industry is a pet peeve of mine. And while I’m exposing my soul, I might as well admit to being a bit of a speciesist. I like the exceptions best when they involve Homo sapiens, so the last exception for today has to do with our own uses for a deoxy-L-sugar, fucose. I must admit that several uses of fucose apply to many mammals, but being the speciesist that you know I am, I ignore them to focus on humans.

Fucose (6-deoxy–L-galactose) is crucial for the turning of an unloved spermatozoa and a lonely oocyte into very premature teenager. Both the development and maturation of gamete cells and the development of the embryo depend on the recognition and communication of surface molecules that include fucose. But wait, there’s more.


The H antigen is linked to the red blood cell through a fucose
residue, but not in the “h” antigen mutant. Because of this, it
is not recognized for modification to the A or B antigen, and
the typical H antigen is not there to prevent development of
the H antibody.
Fucose is also a component of many glycans, including substance H. Also called the H antigen, this molecule is a precursor to the A and B antigens found on red blood cells. For people with A, B, or AB blood, the H antigen is modified to become the mature A or B antigen, but in people with O blood, the H antigen doesn’t mature and remains an H. Therefore, principal factors in every human’s development and physiology are determined in part by a sugar that we shouldn’t be using – according to the rules anyway.

However, not all is goodness and light when it comes to fucose. Some folks have a mutation in their H antigen gene that prevents its maturation to the A or B antigen. All cells would have the mutant H antigen, called h. This is different from being type O (meaning not having any A or B antigen, but still having the H antigen).

The hh or Oh blood type is called the Bombay type, and is very rare. Bombay individuals can donate blood to anyone, regardless of blood type (because they do not express any antigen to be attacked). However, because they make A, B, and H antibodies, they can receive blood only from another person with Bombay blood type. Since Bombay occurs about three times in a million births – good luck with that search for blood.

Let’s tackle the nucleic acids and their exceptions starting next week. By training I am a molecular biologist; I know an exceptional number of nucleic acid exceptions.


Shimizu T, Takaya N, & Nakamura A (2012). An L-glucose catabolic pathway in Paracoccus species 43P. The Journal of biological chemistry, 287 (48), 40448-56 PMID: 23038265

Toxvaerd S (2009). Origin of homochirality in biosystems. International journal of molecular sciences, 10 (3), 1290-9 PMID: 19399249
 
For more information or classroom activities, see:

Bombay blood type –

Glycosides –

Racemization –
http://journalofcosmology.com/SearchForLife108.html