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Enzymes

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Celebaelin
74120.  Tue Jun 13, 2006 4:38 am Reply with quote

In a desperate bit to be the first to set up a specially written 'E' topic I've decided to post this quickly whilst various other threads are being transferred into the shiny new E Series Forum.

Enzymes are so named because the biochemical catalysts the term refers to were first found in yeast, which is en syme/sime from the Greek (no surprise there then). Questions about enzymes in biological washing powders not being 'en simes' because they're not found in yeast suggest themselves. More enzyme stuff will doubtless follow as it occurs to me.

 
Gray
74125.  Tue Jun 13, 2006 4:50 am Reply with quote

Very good - I like the topic. After all, what would we do without them?

Maybe we could work in the QI fact that all our enzymes (and the corresponding molecules in all life on this planet that gets digested) are 'left-handed'. For each possible chemical formula for an organic compound there are nearly always a pair of possible structures that are mirror images of each other, like a pair of gloves.

If you think of a tasty molecule of food as a hand, and the enzyme that exists to digest it as a glove, then in nature, only 'left gloves' and 'left hands' exist.

If a race of hungry aliens came to our planet demanding food, but life on their planet happened to have evolved using the right-hand versions of the molecules, they wouldn't be able to digest any of the food on our planet - they could chew it up pretty well, but it would give them terrible indigestion...

 
Celebaelin
74132.  Tue Jun 13, 2006 5:04 am Reply with quote

That's not quite true though Gray, Cellulose for example is composed mainly of beta 1-4 D linkages between glucose and 'cellulase' (β 1-4 D Gallactosidase) is a perfectly respectable if slightly rare enzyme.

The biologically active amino acids are indeed all L but the biologically relevant sugars, if memory serves and I'll check this in a moment, are all D stereoisomers.

Quote:
Chirality in biology

Many biologically-active molecules are chiral, including the naturally-occurring amino acids (the building blocks of proteins), and sugars. Interestingly, in biological systems most of these compounds are of the same chirality: most amino acids are L and sugars are D. The origin of this homochirality in biology is the subject of much debate. Many chiral drugs must be made with high enantiomeric purity due to potential side-effects of the other enantiomer. (The other enantiomer may also merely be inactive.) Consider a racemic sample of thalidomide. One enantiomer is effective against morning sickness while the other is teratogenic. Unfortunately, in this case administering just one of the enantiomers to a pregnant patient would still be very dangerous as the two enantiomers are readily interconverted in vivo. Thus, if a person is given either enantiomer, both the D and L isomers will eventually be present in the patient's serum. Steroid receptor sites also show stereoisomer specificity.

http://en.wikipedia.org/wiki/Optical_isomerism

This article also reminded me of the R/S system of denoting chirality which is QI in a science nerd kind of way.

I've said all (biologically relevant) amino acids are L and sugars are D, this may not be strictly true but it may be a question of erring on the side of caution by other authors. I'll look out for specific examples of D amino acids and L sugars but none spring readily to mind.

 
dr.bob
74140.  Tue Jun 13, 2006 5:32 am Reply with quote

I attended a lecture on chirality at an alumni meeting at my old University once (I may have mentioned this before). During the course of the lecture, I learned two interesting things.

Firstly, although optical isomers are chemically identical, as Gray points out our enzymes are unable to process half of them that are the wrong way round. A consequence of this is that you can create sugar with no calories. If you produce sugar artificially to only select the optical isomer which the human body cannot metabolise, it still tastes exactly like sugar, but it doesn't cause you to put on weight. Sadly, such artificial production is currently prohibitively expensive.

Secondly, the molecule which makes oranges smell orangy and the molecule which makes lemons smell lemony are optical isomers. Chemically they are identical, but because of their chirality the human olfactory system processes them slightly differently giving rise to different smells.

 
Gray
74142.  Tue Jun 13, 2006 5:33 am Reply with quote

Ah, so a molecule with one 'handedness' can be converted into the other? You'd think that would be an unnecessary complication in a biological system. But then I suppose we're full of those as well. Evolution is not known for her planning ability...

 
Celebaelin
74144.  Tue Jun 13, 2006 5:39 am Reply with quote

Oranges are mirror images of lemons! Superb!

wrt amino acids this seems to cover it quite well and even mentions glycine which has no stereoisomer as is has two hydrogen atoms bound to the α (alpha) carbon

Quote:
Optical Properties of the Amino Acids

A tetrahedral carbon atom with 4 distinct constituents is said to be chiral. The one amino acid not exhibiting chirality is glycine since its '"R-group" is a hydrogen atom. Chirality describes the handedness of a molecule that is observable by the ability of a molecule to rotate the plane of polarized light either to the right (dextrorotatory) or to the left (levorotatory). All of the amino acids in proteins exhibit the same absolute steric configuration as L-glyceraldehyde. Therefore, they are all L-α-amino acids. D-amino acids are never found in proteins, although they exist in nature. D-amino acids are often found in polypeptide antibiotics.

http://www.indstate.edu/thcme/mwking/amino-acids.html

It is perhaps worth emphasising that the chirality we're talking about is with regard to the α carbon, the peptide backbone carbon, not any other R-group (side chain) carbon. The alpha carbon is the one below the COO- and to the right of the +H3N in the illustrations.

 
grizzly
74149.  Tue Jun 13, 2006 5:53 am Reply with quote

I don't really know much about the issue of right handed V left handed enzymes but this article seems to go some way to explain why only one occurs biologically:

http://www.newscientist.com/article/mg19025545.200.html

 
Gray
74152.  Tue Jun 13, 2006 5:59 am Reply with quote

The molecule for the smell of spearmint is the same formula - but a mirror image - as that for the smell of caraway.

So, if I understand the above, it's the proteins that are all L, but the sugars are often R. Does this mean that if aliens came to eat us, they'd get fat and hyperactive, and all their teeth would fall out, but they wouldn't get muscly?

 
Celebaelin
74156.  Tue Jun 13, 2006 6:07 am Reply with quote

Gray wrote:
Ah, so a molecule with one 'handedness' can be converted into the other? You'd think that would be an unnecessary complication in a biological system. But then I suppose we're full of those as well. Evolution is not known for her planning ability...


This image shows the difference between L and D glucose.



Quote:
Isomers

Glucose has 4 optic centers which means that in theory glucose can have 15 optical stereoisomers. Only 7 of these are found in living organisms, and of these galactose (Gal) and mannose (Man) are the most important. These eight isomers (including glucose itself) are all diastereoisomers in relation to each other and all belong to the D-series.

An additional asymmetric center at C-1 (called the anomeric carbon atom) is created when glucose cyclizes and two ring structures, called anomers, can be formed α-glucose and β-glucose. They differ structurally in the orientation of the hydroxyl group linked to C-1 in the ring. When D-glucose is drawn as a Haworth projection, the designation α means that the hydroxyl group attached to C-1 is below the plane of the ring, β means it is above. The α and β forms interconvert over a timescale of hours in aqueous solution, to a final stable ratio of α:β 36:64, in a process called mutarotation.

http://en.wikipedia.org/wiki/Glucose

Woah! I was spectacularly wrong for a moment there! I was off on one confusing L and D forms with anomers which is probably a typical biologists mistake. Aaaaaaanyway to clarify the point about a chiral carbon is that it is not superimposable on the other optical form by rotation. In this digram if you were to switch the positions of the green and the blue 'atoms' you could not rotate the molecule in space to reinstate the original. If any two of the four bonded 'atoms' were the same 'colour' then you could do so. Conversion between L and D forms implies a chemical process.



The link gives thalidomide as an example of a molecule that can be changed in vivo from L to D but it is not obvious to me how this might happen. I would guess that chemical switching in position of H and OH groups is the explanation but I'll have to keep digging for confirmation.

Thalidomide


<E> The first link below is a general description of optical isomerism. The images are not available but the chiral centre of thalidomide is shown in the second link (from the same site). S thalidomide is the harmful one (the teratogen).

<E> Forgot to put in the links!

http://www.chm.bris.ac.uk/motm/thalidomide/opticaliso.html

http://www.chm.bris.ac.uk/motm/thalidomide/optical2iso.html


Last edited by Celebaelin on Tue Jun 13, 2006 7:09 am; edited 2 times in total

 
Celebaelin
74159.  Tue Jun 13, 2006 6:42 am Reply with quote

Gray wrote:
The molecule for the smell of spearmint is the same formula - but a mirror image - as that for the smell of caraway.

So, if I understand the above, it's the proteins that are all L, but the sugars are often R. Does this mean that if aliens came to eat us, they'd get fat and hyperactive, and all their teeth would fall out, but they wouldn't get muscly?

L and D are not related to R and S except that they both describe chirality. L and D does it by the rotatory affect on polarised light, R and S does it by atomic number of the atoms around the asymetric carbon.

 
suze
74163.  Tue Jun 13, 2006 7:06 am Reply with quote

Ah, optical isomers and stuff. I haven't studied chemistry since High School, but I always found it Quite an Interesting subject.

Could I just intrude for a moment and ask a question about terminology? Why there are three different ways of classifying optical pairs? The D/L and R/S dichotomies have already been mentioned, but in my school days we were taught the d/l system (which I gather is different from D/L). Isn't it actually d/l which refers to the effect of polarized light, while D/L is something else that I don't really understand?

Anyone would think the chemists were trying to make things complicated so that the rest of the world left them alone!

I understood cis-trans isomers perfectly ...

 
Celebaelin
74166.  Tue Jun 13, 2006 7:24 am Reply with quote

From Wiki (for link see post 74132 above in this thread).

Quote:
The D/L labeling is unrelated to (+)/(-); it does not indicate which enantiomer is dextrorotatory and which is levorotatory. Rather, it says that the compound's stereochemistry is related to that of the dextrorotatory or levorotatory enantiomer of glyceraldehyde. Nine of the nineteen L-amino acids commonly found in proteins are dextrorotatory (at a wavelength of 589 nm), and D-fructose is also referred to as levulose because it is levorotatory.


I didn't remember that but I have a sneaking suspicion that I was told it at school.

Quote:
* R from Latin rectus meaning upright, or
* S from Latin sinister meaning left


While the optical rotation of glyceraldehyde is (+) for R and (-) for S, this is not true for all monosaccharides. The stereochemical rotation can only be determined by the chemical structure, whereas the optical rotation can only be determined empirically (by experiment).

Monosaccharides with an identical conformation at the last stereocentre (eg. C5 for glucose) to (R)-glyceraldehyde are assigned the stereo-descriptor D, those similar to (S)-glyceraldehyde are assigned a L. Both D and L should be small capital letters.

http://en.wikipedia.org/wiki/Glyceraldehyde

I didn't however know that L and D were allocated on the basis of the R and S forms of glyceraldehyde (and don't stand for levorotatory and dextrorotatory) or indeed that they should in fact be SMALL CAPITALS.

So l and d presumably, and I can find no reference to this, do indicate levorotatory and dextrorotatory.

I knew there was a reason I liked it here.

<E> Look another way!
Quote:
levorotatory

ADJECTIVE: Symbol l
Of or relating to an optically active chemical that rotates the plane of polarized light to the left, or counterclockwise: Only levorotatory amino acids are biologically active.

http://www.bartleby.com/61/12/L0141200.html
http://www.thefreedictionary.com/levorotatory
http://www.yourdictionary.com/ahd/l/l0141200.html
Quote:
dextrorotatory.

adj. Symbol d-
Of or relating to an optically active chemical that rotates the plane of polarized light to the right, or clockwise: a dextrorotatory solution.

http://www.thefreedictionary.com/dextrorotatory
http://www.bartleby.com/61/79/D0187900.html
http://www.yourdictionary.com/ahd/d/d0187900.html


Last edited by Celebaelin on Tue Jun 13, 2006 7:37 am; edited 3 times in total

 
Tas
74168.  Tue Jun 13, 2006 7:27 am Reply with quote

I'd just like to point out that I have understood very little of this, but am struggling to keep up. It is QI.

:-)

Tas

 
samivel
74213.  Tue Jun 13, 2006 9:43 am Reply with quote

ditto

 
ficklefiend
74619.  Wed Jun 14, 2006 1:48 pm Reply with quote

dr.bob wrote:
If you produce sugar artificially to only select the optical isomer which the human body cannot metabolise, it still tastes exactly like sugar, but it doesn't cause you to put on weight.


Wow, I might even accept an offer of Splenda next time I'm taking tea. (I was convinced it would do something horrible to me, but now I understand.)

 

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