Talk:Macromolecular chemistry/Draft

Editing discussion version 1

Reverse anything Robert. A question do we follow US spelling. On links polymerization or polymerisation. I dislike Zs but I crrently believe CZs using zeds. David Tribe 19:43, 27 January 2007 (CST) Nah David, there is no need for reversal of anythin, thanks for your contribution and rectifying my caps - somehow I feel/felt capped words do seem more appripriate to be linked than non capped. About the english/US spelling, both are ok with me but since this is mostly us-based I merely adapted :). Another argument can be that the mojority of literature is from the us - and using US-zeds. (My books were over 90% from the states during study and promotion. Some were in german - as translation from russian research.) By the way - and totally irrelevent this is - to me - a work in progress I type new stuff (all by heart) when I feel to it - knowing the majority of the material about macromolecules will be outside this piece as it is way too complex to describe and explain here. Question: how did you tackle that problem in biology in relation to chemical biology, biochemistry, structural biology and these rather exact sides of biology? Thanks, Rob. Robert TitoRobert Tito 19:59, 27 January 2007 (CST)

Can't be very helpful as the things Ive worked hard at were all different. The Biology article was largely started by Nancy who nicely encouraged a group effort and it is an ambitious general introduction, my efforts on Wheat were on a fairly easy topic, and all by myself, like you here, Horizontal gene transfer and RNAi are more technical (with lots of reference work), Ive dabbled in Microorganisms, and really want to work up Plant breeding very well. You can learn different things from each of those experiences - eg final editing of the current Biology/Draft. But I can help bring some of that experience across because I'm not a chemist as such but I do have done a lot of biochemistry experience. Your typing by heart is making it simple to read and clean in style. I can see perhaps English is not your natural language (or that you are, like me, not a perfect quick typist), and happily make some minor adjustments/ suggestions for you if I get time, but the flow of your English is very good. Ill return hopefully with better answers David Tribe 16:32, 30 January 2007 (CST)

No pictures!?

How can an article get approved with not a single picture? There has to be something we could add. -Tom Kelly (Talk) 22:28, 17 February 2007 (CST)

I'm sure the polymer chemistry professors have some cool pictures. Can we find some? -Tom Kelly (Talk) 22:31, 17 February 2007 (CST)

What about a figure to illustrate a functional group? -Tom Kelly (Talk)

Couldn't we get a Hb H-bond / ionic bond / pic? -Tom Kelly (Talk) 22:32, 17 February 2007 (CST)

Metal Rxn / enzyme lock and key picture? -Tom Kelly (Talk) 22:33, 17 February 2007 (CST)

MW

Large (macro) - can we get a MW range? -Tom Kelly (Talk) 22:34, 17 February 2007 (CST)

Biopolymer notes

Biopolymer notes David Tribe 20:48, 27 January 2007 (CST) See:

• Genencor International and DuPont Expand R&D Collaboration to Make Key Biobased Polymer
• DuPont Engineering Polymers Previews Plans to Produce a New Family of High-Performance Polymers Made with Renewable Resources

Leads with: DuPont Engineering Polymers Previews Plans to Produce a New Family of High-Performance Polymers Made with Renewable Resources

QUOTE CHICAGO, June 20, 2006 — DuPont Engineering Polymers today announced at NPE that it is moving forward with plans to produce a new family of high-performance thermoplastic resins and elastomer products made with renewable resources.

The new products are DuPont™ Sorona® polymer and DuPont™ Hytrel® made with renewable resources. The key ingredient in Sorona® is Bio-PDO™, which is derived from corn sugar using a patented and proprietary fermentation process. Bio-PDO™ is a replacement for petrochemical based 1,3-propanediol (PDO) and/or 1,4-butanediol (BDO). DuPont™ Hytrel® made with renewable resources will be produced using a new DuPont polyol made with Bio-PDO™.

DuPont™ Sorona® with Bio-PDO™ will be available mid 2007; and DuPont™ Hytrel® with renewable resources will be available 4th quarter 2007.continues Polylactide (to follow) David Tribe 20:48, 27 January 2007 (CST)

contributions

Feel free, authors and editors, to add to the macromolecular article to create a starting point to talk all about macromolecules, with the generic piece being this macromolecular part and the related (to be written) pages as its siblings.

Robert Tito | Talk 08:54, 17 February 2007 (CST)

my nickel

This article, overall looks great. It may be to late to make suggestions about language for this edition, but here are a few minor points. In the second paragraph, just after explaining DNA and proteins are macromolecules: The value of macromolecules specially in the form of polymers and plastics has risen tremendously during the last 60 years. Obviously what is meant is the value in 'manufacturing and technology', or something to that effect- just to emphasize the diference between man-made molecules (including even DNA etc in biotechnology) and the value of macromolecules in nature, which has been pretty steady on earth for a lot longer than we've been around.:-). That distinction of manufactured v native molecules might be carried out through the text. Shall I give it a try? Nancy Sculerati MD 06:27, 27 February 2007 (CST)

Have we decided to put requests for approval on the article itself now? I don't think they really belong there, for the simple reason that we don't want to mislead people into thinking that the article has been approved already. --Larry Sanger 08:13, 27 February 2007 (CST)

I'm certainly no chemist, so please check what I intended as simple copy edits carefully. I'd like to see a couple more illustrations, perhaps one might be of a lipid bilayer? Some sentences I just didn't understand - e.g. "These units are not per definition equal to the repeating monomeric unit in, for instance, polypeptides"Gareth Leng 08:19, 28 February 2007 (CST)

my zac's worth

I think its good enough to be approved without embarrassment, but acknowledge and expect it to make significant further progress as the stylists descend upon it. One bilayer or emulsion diagram schematic could be usefully added tho'. Ill probably do no more (being a mere biochemist).David Tribe 15:13, 28 February 2007 (CST)

Carbohydrates

I have two quick comments. The following sentence occurs twice: "Biological macromolecules include proteins, nucleic acids (DNA and RNA) and enzymes. " Why the reason to have both protein and enzyme? This seems quite redundant. Was it done to distinguish ribozymes, and even so, that would be redundant with the RNA?

I would propose getting rid of enzyme and added polysaccarides. Cellulose is probably the most abundant macromolecule on Earth. it would be strange not to mention that class. Chris Day (Talk) 15:48, 28 February 2007 (CST)

Re: my second point i see that Robert added polysaccarides into the biological molecules. It currently reads:

"'The best known biological macromolecules are deoxyribonucleic acid (DNA), ribonucleic acid RNA, proteins, enzymes, cellulose and polysaccharides."

I would suggest a simpler sentence as follows:

"The best known biological macromolecules are nucleic acids (DNA and RNA), proteins and polysaccharides."

If there is no objection I will change this in both the lead and the biological molecules section. Chris Day (Talk) 10:51, 1 March 2007 (CST)

Sounds right to me Chris. Rob - please check my edits, I've tried to interpret the chemistry but I'm no chemist so may have messed some things up. Please revert anything you don't like without any hesitation at all.Gareth Leng 10:55, 1 March 2007 (CST)

I can see the omission of cellulose, but I regarded them from the point of view of some reader without any deeper knowledge, enzymes and cellulose are terms people have heard - and from a 'teaching' point I left them in. How many persons actually KNOW enzymes to be proteins? Maybe it should be changed into proteins and special proteins such as enzymes. For me important: people should be able to learn things they didn't know before. Actual things being more important to scientific fundament - that should be covered in detailed pages. If persons get triggered they might look it up in these pages. Robert Tito | Talk 11:13, 1 March 2007 (CST)

heyyyyyyyy before altering let me respond to your suggestions :) sheesh speedy gonzales you two are. this is europe, you hear :))) Robert Tito | Talk 11:30, 1 March 2007 (CST)

I hear you. I intend to incorporate the enzymes and cellolose teaching attribute as a second paragraph in the biological macromolecules. (side note, your edits, Robert, don't appear for me unless I enter edit mode. This is very strange since Gareth's edit do not suffer from the same problem, so it appears not to be a cache problem. I have noticed this a few times now, but only for your edits, no one else). Chris Day (Talk) 11:41, 1 March 2007 (CST)

As have I for several persons, and sometimes myself as well. still the cache error I assume Robert Tito | Talk

Yep, even this last edit didn't show for me. So you're not going crazy Chris. And Robert, they listen but your edits don't show until someone edits again. You are still in stealth mode again:) Matt Innis (Talk) 12:34, 1 March 2007 (CST)

this is not just stealth mode, this is 007 mode, and I must wanr you, I am licensed to 007 Robert Tito | Talk ok let me do some garbage collection in macromols befire I set out to execute according to my license. please do not edit, else you will be put onto that list :) now it is DINNER time first. Robert Tito | Talk 12:44, 1 March 2007 (CST) Somehow the link between proteins and enzymes (obvious for biochemists and biologists) is still lacking. I will see how I can iron that into the text somewhere. It must be obvious for all, at least after reading this, that enzymes are proteins with a specific function. It is like all this commercials talking about cholesterol, nobody has a clue cholesterol is essential, and for what purpose they are essential. (not forgetting to mention the total BS about trans fats (where the chemical definition of trans as opposed to cis seems to be a commercial misnomer and a BAD OMEN. People get disinformed by this kind of info, as it adds nothing to it. cheers BACK into the kitchen, still cooking dinner. And I am about to eat it Robert Tito | Talk 13:58, 1 March 2007 (CST)

the new biological groups added

I wonder if they really contribute much - besides telling something about their chemistry. the ribonucleotides - ok seen as another polymerization result from phsphate and two sugars (coincidentally transporting a genetically important functional group). Else I think they belong on their more detailed pages in sections where these are dealt with in depth. Robert Tito | Talk 14:26, 1 March 2007 (CST)

I was trying to emphasis some of the chemistry involved as well as function. I have no problems with exporting to other pages. The problem I have at the moment is that there is very little actual chemistry on the biological mamcromolecules, or it is splintered throughout the article. If there is to be a biological macromolecules section, it should at least address the chemistry. Possibly that means stripping it from other sections in the article? In my opinion, the article is currently top heavy on biological function rather than chemistry. Chris Day (Talk) 15:28, 1 March 2007 (CST)

yes as per my choice. the chemistry of polymers will be alot harder to read - as that will contain the physico-chemical implications and these are less easy to read as most are explained and accompanied by a somewhat dry set of equations. Here as a first introductory page I wanted to sjip anything that resembles physics, maths or anything too abstract to understand. I did try and still think this page should be aimed at everybody, no matter what background. And its goal should be: making people think themselves about these strange molecules and visualize the molecules in their mind. If you present any pictuyre or diagram that personal view is forced to run through paths made by the painter of the picture. (compare LOTR - the book and LOTR the films) Robert Tito | Talk 15:37, 1 March 2007 (CST) As example: I could start using the free enthalpy and using entropy-limitations create an integral to calculate the likely shape of a certain polymer. I wonder how many people will still read it after the first sentence. Robert Tito | Talk 15:42, 1 March 2007 (CST)

I agree we want to make it user friendly. I tried to do this with the polynucleotides section. I was thinking of a similar style/content for the other three. I agree its dry, but the title does say chemistry; a minimum should be to describe the repeating units and the bonds that hold them togther. In addition the biological significance should be outlined. For example, RNA and DNA are informational and must be copied from a template. Certainly we should avoid bioenergetics. Chris Day (Talk) 15:49, 1 March 2007 (CST)

things that are informatirve as well as 'chemical' in nature are for instance the coiling, super coiling and ultimately collapsing of DNA molecules into the tightly packed molecules that can be made visible without many extreme measures. I will see where that can be ironed in Robert Tito | Talk 15:54, 1 March 2007 (CST)

chemistry templates

I will add the ability to treat a polyelectrolyte like any acid or base and tritrate them, determiniung the concentration. The direct and indirect light dispersion of macromolecules as function of the deflection angle representing the shape of molecules. The electrochemical nature of macromolecules, for instance in their usage as liquid chrystals, biological computers and the solvatation behavior. And biological funstions performed by DNA, transcriptases upon unbalances in cells of certain chemicals, triggering the transcription of DNS into RNA into proteins to enhance a certain response by the cell to counteract the unbalanced reacion that was the trigger in the first place. Robert Tito | Talk 16:34, 1 March 2007 (CST)

All your ideas above seem interesting. i'm done for now Robert so bash away some more if you have time. I'm not that happy with everything I have written but it gives us a frame work. Sorry for adding all this when you were close to aproving. Chris Day (Talk) 16:57, 1 March 2007 (CST)

One thing that i have not really addressed is the redundancy with what I wrote in the biological macromolecules section and the functional section at the end. At present I have not even tried to address this issue but will work on it next if others don't beat me to it. Chris Day (Talk) 17:00, 1 March 2007 (CST)

conflict?

Despite cellulose being the most abundant macromolecule on Earth, it is of limited use to animals as a food source due to the lack of an appropriate enzyme to cleave the ?-glycosidic bond. Ruminants, such as cows, can digest cellulose in their second stomach by co-opting bacteria to digest the cellulose. Common polysaccharides that are digestible by animals are starch and glycogen and both use an ?-glycosidic bond to join the glucose molecules together. Animals do have enzymes that can hydrolyse the ?-glycosidic bonds of these polysaccharides into their glucose monomers. what is ? what is ? Robert Tito | Talk

? should be a beta and  ? should be an alpha, I assume they are not showing up like that in your browser? Chris Day (Talk) 23:41, 1 March 2007 (CST)

Are neuropeptides a good example?

We currently have the following example:

"For example, neurons make many different receptor molecules, that are present in the cell membrane. These molecules bind specific messenger substances, and when these messengers bind to the receptor molecule, this triggers a biochemical response within the neuron. The binding of a messenger substance to a receptor molecule depends on both the physical shape of the receptor molecule and its composition."

Firstly, are the neuropeptides large enough to be considered as macromolecules? second, in the introduction we currently have CJD and alzheimers as an example of changes in conformation. Another possible example is to continue with the hemoglobin theme and use sickle cell anemia. However, I'm not sure any of these really give the kind of subtle example that is actually more dramatic. Couldn't we use temperature sensitive alleles as an example here? A particularly dramatic, and well known example, is seen in siamese cats.

L. A. Lyons, D. L. Imes, H. C. Rah, R. A. Grahn (2005)

Tyrosinase mutations associated with Siamese and Burmese patterns in the domestic cat (Felis catus)

Animal Genetics 36 (2), 119–126.

From the paper:

"The Siamese cat has a highly recognized coat colour phenotype that expresses pigment at the extremities of the body, such as the ears, tail and paws. This temperature-sensitive colouration causes a 'mask' on the face and the phenotype is commonly referred to as 'pointed'. Burmese is an allelic variant that is less temperature-sensitive, producing more pigment throughout the torso than Siamese. Tyrosinase (TYR) mutations have been suspected to cause these phenotypes because mutations in TYR are associated with similar phenotypes in other species........the SNP associated with the Siamese phenotype is an exon 2 G > A transition changing glycine to arginine (G302R)"

The temperature senstive mutation is in one of the pigment synthesis genes (Tyrosinase). At high body temperature it is not functional yet in the cooler extremities it can still function normally. Chris Day (Talk) 23:54, 1 March 2007 (CST)

The example is not of neuropeptides (many of which are not really large enough to be regarded as macromolecules) but of their receptors, which certainly are. Maybe illustrations of a receptor molecule would make the point better? I like the receptor example because it's possible to imagine how a small conformation change can affect function; the cat example is an interesting example but I don't have any intuitive understanding of the mechanism that produces a change in function. I've extended this to clarify; but if the example isn't great please just cull it ruthlessly - I'll take no offence at all. But do the receptors really count as macromolecules in the relevant sense??Gareth Leng 04:06, 2 March 2007 (CST)

I see it now, I did not parse that correctly. This makes more sense, although, one issue I have here is that these are subtle changes that modify binding affinity, but are they due to different conformations? Couldn't the different receptors have different amino acid residues in the binding site? I am not familair with the specific examples so i can't judge this accurately. For the Tyrosinase example, the mutation definitely alters conformation. The point mutation destabalizes the conformation such that the active site can no longer function. Even more extreme, for the CJD example, the conformation is completely different, mostly alpha helix in normal conformation but mostly beta sheet in the disease state. For me, at least, it is clear that these last two examples are relevant to conformation.

For receptors, it seems that a more important conformation component of the example is that there is a significant conformation change due to the ligand binding. This chnage in conformation is required for the function of propagating a signal through the membrane. This aspect of the example is distinct from the binding affinites of the various ligand/receptor variations. Chris Day (Talk) 10:38, 2 March 2007 (CST)

If the leptin receptor is all one (or mostly) one big molecule, then I think it does. Perhaps we can add a line that lends emphasis to the receptor v the ligand. I'm going to try, but since I'm no expert at the science you may have to throw out what I write-or change it. I think, looking at CZ as a whole, that mentioning the Tyrosine receptor might be nice (if we have room). We can use the cat picture and we can link to Cat colors. There are other color genes that appear to be temperature sensitive too, see Horse colors. The "points" of horses are also inherited, but I'm not sure that the molecular biology is understood as well, exactly how this EE gene works. I was also thinking- maybe we can use complement to sort of show how smaller molecules can assemble into a macromolecule that then functions according to its new conformation. Nancy Sculerati MD 06:58, 2 March 2007 (CST)

A good example might be of the GABA-A receptor, which has four subunits, some of which are variable, and different compositions give different affinities for benzodiazepine and allogregnanoloneGareth Leng 10:28, 2 March 2007 (CST)

This would be an excellent example of composition, I think this would be an excellent example to add? Chris Day (Talk) 10:36, 2 March 2007 (CST)

keep in mind

this is about the CHEMISTRY of macromolecules, not the biology or biochemistry (the latter having more relations to the chemistry as the former). Robert Tito | Talk 10:42, 2 March 2007 (CST)

I agree andf think the biological examples are begining to dominate. My only reason for expanding the biological molecules section was too discuss the monomers and to touch on the chemistry of the linkage bonds. Certainly the conformation and configuration should not be all about proteins. Chris Day (Talk) 11:00, 2 March 2007 (CST)

Me too. Just chipping in with what I knew about, which isn't enough I know, but I make sense of things by relating them to things I know a bit about. Why not clear out anything that's in excess and create a stub? Gareth Leng 11:26, 2 March 2007 (CST)

Nevertheless, the topics you added have a value - I will have to see (using helicopter view mode) where the balance now is. Probably - and I say this before reading everything in detail - some can stay in place, with an additional link to appropriate articles where the details will be or are covered. cheers Robert Tito | Talk 11:30, 2 March 2007 (CST)

Fine. I added the bit about overeating just to make sure your obsssion with DINNER is under control.Gareth Leng 11:34, 2 March 2007 (CST)

This following sentence does noit seem to make sense. It seems to be refering to the ligand as a receptor? Or am i missing something obivous?

"For example, leptin is a 16 kDa peptide hormone produced by fat cells that signals to the brain to report the level of energy stores in the body; it acts at a leptin receptor expressed in the hypothalamus (and elsewhere). "

I find it strange that we have alzheimers in the intro but it is never to be mentioned again. Possibly adding a sentence after leptin to discuss that huge conformation change can cause real problems leading not only to misfunction but to toxic consequences? Chris Day (Talk) 11:48, 2 March 2007 (CST)

Forget this comment i just realised that i read the bolded at above as an as. Still it would be good to know if this is an example of a conformation change as opposed to a specificity issue (i.e. critical residue for interatction at the receptor missing) Chris Day (Talk) 21:37, 2 March 2007 (CST)

An example of influences of CONFORMATION is an example Robert Tito | Talk 21:43, 2 March 2007 (CST)

hydrogels

i just realised that this topic is absent from the article. It has a biological aspect since plant cell walls can act as hydrogels. Depending on the salt concentration in the xylem vessels the cell wall either expands or shrinks. Such changes are used to regulate the bulk flow of liguids through the plant. I am pretty sure this is a hot topic in cemistry/engineering too, from a synthetic perspective, although I do not pretend to know anything about this topic. Chris Day (Talk) 12:13, 2 March 2007 (CST)

I just did a quick search for them inthe news and found this recent article.

http://www.rsc.org/chemistryworld/News/2007/February/22020702.asp

This seems to fit nicly with the section here that talk about the molecular memory. Another article mentions hydrogels in the context of contact lenses.

http://www.usnews.com/usnews/health/articles/070225/5lens.htm

This might jazz up the real world conections for a general audience. Chris Day (Talk) 12:24, 2 March 2007 (CST)

Balance

I think it is reading pretty fluently , and although all the suggestions are good, Roberts point about balance is right on target. We don't need another Biological article. Deliberate searching for non bio balance is needed. David Tribe 20:39, 2 March 2007 (CST)

One solution is to start migrating some of the content out to other more biologically relevant articles. Chris Day (Talk) 21:26, 2 March 2007 (CST)

If you enthusiasts give me some TIME to read/think, reread and do some editing I can do that, unfortunately you dont leave me the time to do that :)

Let the artricle rest for saturday and I will take a look at it, do some rewriting when necessary - and copy parts to the talk page that should be handled somewhere else in (far) more detail,. That leaves me some time to do it at peace, and sunday the article is up and runiing for all the predators :))) And do not forget the time zones. Robert Tito | Talk 21:31, 2 March 2007 (CST)

state of the text

As of now I would like to request no more large additions to the text and only small grammatic enhancements. What is needed however are pictures depicting the variety of molecules described, and why in heavens name they are called alpha, betam, 6,6 and such. Someone without any knowledge or organic chemistry will be bewildered by all these strange latin sounding names. Overall the text now bears a nice mixture of a variety of chemical behavior all attributed to the macro-nature of some molecules. There is somewhat too much emphasize on the bio-side but I think that will serve the purpose of understanding the nature of their interactions and what mechanisms are hidden behind it. Robert Tito | Talk 10:58, 3 March 2007 (CST)

Looking good! I performed a once through for spelling and grammer and noticed a couple things you might want to look at. 1)There is mention of condensation reactions in the Nylon and DNA sections but it is unclear what condensation reactions are (for the sake of the uninformed they aren't mentioned elsewhwere). 2)we use a mix of -ise and -ize occasionally throughout. I know this is a US/British thing that I guess you need to decide which you want so keep an eye out.

leptin

I have removerd the following paragraph:

"Slight changes in the conformation of a receptor molecule or an enzyme can make them dysfunctional. For example, leptin is a 16 kDa peptide hormone produced by fat cells that signals to the brain to report the level of energy stores in the body; it binds specifically to a leptin receptor expressed in the hypothalamus (and elsewhere). Some mutations in the leptin receptor prevent the leptin from binding and the signal is blocked. As a result, the individuals affected by this mutation compulsively overeat and become grossly obese. Leptin: Your brain, appetite and obesity

I have read a few of the papers about these mutations and they seem to be more dramatic than alterations in conformation. For example, the fatty mutation mentioned in the cited reference is a deletion of the cytoplasmic domain of the fatty gene (fa). There is no mention of conformation changes. If we use examples we need to be sure they are actually examples of hypomorphic alleles that display changes in conformation. Next question is do we need specific examples? Chris Day (Talk) 17:21, 5 March 2007 (CST)

I am not certain conformational changes were denied, as ANY change in composition automatically lead to a changed conformation. I would like as example to have it added, maybe less emphasizing conformation but more as possible due to configurational change. They seem related in every publication I read. Robert Tito | Talk