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

Wrong definition of macromolecule

From the introduction this article sets off on the wrong foot:

A macromolecule is a molecule that consists of repeated 'building blocks', that may not be identical. When the same building block is repeated, this block is called the monomeric unit (monomer), and the resulting macromolecule is called a polymer, or by its generic name plastic. Nylon is an example of a macromolecule that is an artificial polymer.

First of all, A macromolecule as coined by Staudinger simply infers a covalently bonded molecule with large molecular weight. A building block is the underpinning of a polymer, but not necessary a macromolecule (consider lipids, which are generally classed as macromolecules but do not consist of simple low MW monomers).

Second, polymer and plastic are not synonymous.

Third, polymers may contain dozens of different monomers, such as copolymers and proteins which are simply polymers of amino acids. (See van Holde, K.E. Principles of Physical Biochemistry and others).

Fourth, in the context of biology a "macromolecule" often refers to two or more distinct molecules.

This incorrect definition is proliferated throughout the article.

A correct definition of macromolecule would be "any molecule with large molecular weight, typically over 1000 Daltons, including polymers, lipids, and macrocycles". I will clean this up shortly. Jacob Jensen 01:44, 3 April 2007 (CDT)

Please decide what this article is about

Also, this article lacks focus. From the outside links I suspect that this article is supposed to be about macromolecular chemistry, a subdiscipline of chemistry focused on the synthesis and study of large molecules. I can't find a single section in this article that discusses the discipline (prominent journals, history, active areas of research, etc.) - it seems to be a long list of polymer and biology-related facts which belong in smaller, more focused articles. It might make more sense to redirect this page to the polymer chemistry page and part out the remaining content to other as yet uncreated pages.

Can we part this article out into multiple sub-articles and redirect this particular page to the polymer chemistry article? Jacob Jensen 01:50, 3 April 2007 (CDT)

Jacob, many people worked very hard on this article, and I encourage you to look at Biology, Chemistry before dismemberment begins.;-) . I also encourage you to communicate with Rob Tito on his talk page. He has been stuck as only chemistry editor - and left to deal with a mob of biologists. Why don't you collaborate - and I encourage you to rethink and reedit some of your comments because we try to encourage each other here, and demolition is considered highly discouraging. Also, when we place any sort of cutting remarks, being the gently mannered ladies and gentlemen that we are, we bend over backwords (so to speak) to avoid anything as blunt as "mishmash" or "irrelevant". Not our style, that's - I've been told, the style of that other place. Here we are professional, always, in our behaviour. That means we use only the sharpest instruments,like the thin stilletto that leaves no outward mark- so thin and so very sharp that it can even leave the victim unaware that he (or she) is bleeding. (;; - that's two winks) Rob has a great sense of humor and so I imagine we will all get along. Try it that way, please - I mean the talkpage, not the stilletto. By the way- Rob speaks several (actually many) languages and so I would be a bit gentler about the use of English words here. Again-he has only us humble bio folk to collaborate with, and we aren't likely- half the time-to know enough to use proper words in the eyes of a Chemistry editor whose first language is English. All in all, I hope you'll try talking to us here on the discussion page like you would have talked to your advisor in his office, or if you were on a stage at a meeting. There are ways you can suggest changes very clearly with colleageality and respect. We really are glad you are here. Rather than criticize using the blunt instruments- why not rewrite the above section with an outline of your proposed changes? I assure you there are many concerns, and a positive approach is likely to be welcomed (as will you be, with such an approach) Nancy Sculerati 02:04, 3 April 2007 (CDT)

Thanks, Nancy. I've dropped a note at Bob's talk page (and axed some of the less-than-diplomatic comments - five years in the semiconductor industry does that to a person). That being said, I am still concerned that this page fails to give a novice a "lucid, highly readable [introduction] written in compelling, narrative prose that really does the job of introducing a topic to people who need one". , I have started a macromolecule page which provides referenced definitions of the term "macromolecule" and explains how the usage of the term differs between polymer chemistry and biology. I have also brought up a live polymer page, again with referenced definitions, reflecting substantial revisions to my initial cleanup at wikipedia. I hope that these pages can provide context for future improvements to this article.

As for the content, I suggest that we have a closer look at the activities of professional organizations and journals in the field of macromolecular chemistry to correct the overemphasis on biology. While proteins and other biopolymers meet the definition of "macromolecules", reports on their reactivity, structure, and chemistry still remain the purview of biology and biochemistry. The field of macromolecular chemistry (for largely historical reasons) focuses almost exclusively on synthetic polymers.

In short, there is a lot of good content here which could form the basis for many other pages. In my opinion, however, the content does not serve its purpose as an introduction to the field of macromolecular chemistry. Jacob Jensen 13:06, 3 April 2007 (CDT)

You are likely to be right, and another article with another title-maybe Macromolecular Biochemistry (if there is such a thing) can be split off. So-why don't you make an outline of what you would like to see here, and we bio people can split off -after discussion- what is better in that other article. Please put a proposed plan for this article below- and best to say what you think it is important to focus on, no need to discuss the article as it stands. We'll get Rob's input on your plan (and others) and continue the collaboration.Nancy Sculerati 13:48, 3 April 2007 (CDT)

See the section above titled Balance, we were definitley moving in that direction (Biological macromolecules). Chris Day (Talk) 14:01, 3 April 2007 (CDT)

I think that most of this material belongs in an article entitled Biomacromolecules or Biological macromolecules rather than Macromolecular Biochemistry because (a) the material is about the structure and properties of the macromolecules themselves and (b) because, as you mentioned, no such field is generally recognized to exist. A good place to start for deciding what goes where can be found by perusing the mission statements of various journals of macromolecular chemistry. For example, the ACS journal Macromolecules counts itself as the premier journal of "polymer science", consistent with common usage in the field that fails to differentiate between "macromolecular chemistry" and "polymer chemistry". The mission statement reads, in part:

Macromolecules publishes original research showcasing innovative concepts, experimental methods/observations, and theoretical approaches... focusing on all fundamental aspects of macromolecular science, including synthesis, polymerization mechanisms and kinetics, chemical modification, and solution/melt/solid-state characteristics, as well as surface properties of organic, inorganic, and naturally occurring polymers. [1]

A quick survey of the table of contents for the current issue shows a wide variety of articles about laboratory polymer synthesis - the only mention of a biological polymer is an article about laboratory polypeptide synthesis rather than biosynthesis. I think that the scope of an article on macromolecular chemistry should be consistent with the scope of this journal.

Another prominent ACS journal, Biomacromolecules, puts forth the following mission statement:

Biomacromolecules is an interdisciplinary journal publishing original research that explores the interactions of macromolecules with biological systems and their environments as well as biological approaches to the design of polymeric materials.[2]

Biomacromolecules positions itself "at the interface of biology and polymer science", meaning that overlapping research interests are represented rather than a distinct field.

My proposal is that macromolecular chemistry redirect to polymer chemistry, taking with it some of the non-biological content including the pretty-darn-good-but-still-needs-some-work section on "physical polymer chemistry". The biological content should be moved to one or more articles named biological macromolecules or biomacromolecules.

As a template for the polymer chemistry article I think that we should follow the excellent flagship chemistry page, focusing on the history of the discipline, prominent concepts, journal, and other references. I will propose a more specific disposition for each section shortly.

Comments, please? Jacob Jensen 16:00, 3 April 2007 (CDT)

Go for it. I'll help with the bio page. Chris Day (Talk) 16:04, 3 April 2007 (CDT)

Detailed proposal : redirect to polymer chemistry and create new pages with remaining content

Following on the thread above, here is a detailed proposal for the following:

1. Redirect this article to polymer chemistry, consistent with usage as noted above
2. Move individual sections to existing polymer and macromolecules articles and create new articles plastics and biomacromolecules (or biological macromolecules) based on existing material
3. Ensure that the polymer chemistry article serves to introduce the field of polymer chemistry rather than teach a short introductory course in polymer chemistry.

I have parted out the proposal by section:

1 Macromolecules : fact-check definition, and incorporate into macromolecules article.
2 Economics and Environment : can be moved to polymer, or maybe form the basis for an article on plastics
3 Sources of raw material : also move to polymer or plastics
4 Simple polymers' : general information may be incorporated into polymer - discussion of thermoplasts and thermoharders may be moved to plastics. I think that the terms "thermoplastic" and "thermoset" find more common usage.

5 (Poly)peptide polymers : explain the difference between Nylon and naturally occurring polypeptides. They share a common backbone but few would class nylon as a polypeptide. Move to biomacromolecules
6 Biological macromolecules - move with all subsections to biomacromolecules
7 Introduction to Physical polymer chemistry - move with all subsections to polymer chemistry. Will need some rework but that can come later
8 Functions of macromolecules : Move with all subsections to biomacromolecules, although the text suggests a more generic article on structure and function. Exception: move section 8.4 to polymer as an application for polymers

Provided the first two proposals meet with no objection, I will propose a format for the polymer chemistry article on the related talk page.

Please feel free to leave comments as needed. I will defer making any changes until 6 April to allow other authors/editors the opportunity to respond. Jacob Jensen 16:27, 3 April 2007 (CDT)

Redirection

It is not really appropriate to redirect an article in the main namespace to a subpage of a userpage. Rob, this makes it look as if you are claiming all development of the article to yourself. I'm sure you didn't mean to claim or imply that, but it is how many other people would see it.

Why, by the way, was the article moved, anyway? As long as there are others interested in working on the article, as this talk page seems to indicate, shouldn't the article live here? --Larry Sanger 17:38, 21 June 2007 (CDT)

the article is ready to be appproved. To prevent a very well written article from mutiliation I moved it to my own space. May I remind you it was you preventing approval. And since there are NO other chemistry editors active - it is merely an act of preserving a good scientific document from meddling. When other editors in chemistry become active it can be returned to its place until that time the redirect seems in place to people can at least see the article and know its contents as it is encyclopedian and ready. I would like to see the redirect replaced - so people can add material, changes seem not necessary. Robert Tito |  Talk  18:01, 21 June 2007 (CDT)

Might there be molecular biologists that could jointly approve the article? It's a nice article and it would be a shame to see it go unapproved for lack of chemistry editors. Greg Woodhouse 18:12, 21 June 2007 (CDT)

Greg, the joint approval of a biology editor, and myself (but then I am a major contributor as it is my speciality) did.t seem to be enough - HOWEVER you could make it a one editor approved document. I see you appreciate the prevention move I did - and prevention was all I had/have in mind. Not because I am the major contribuant but people likee: David Tribe, Gareth Lang, Matt Inees, Chris Day all have added necessary parts to make it as easy to understand as it is right now. However that was not enough. As biology editor (molecular biology and biochemistry) they both are linked to chemistry as well as biology so you are able to approve the document. If you wish to do so, I will execute the appropriate move to article space. Cheers. Robert Tito |  Talk  18:26, 21 June 2007 (CDT)

I see. In that case, I've moved the article back to the main namespace. As a general rule, it is not an appropriate goal for CZ to "preserv[e] a good scientific document from meddling" as you put it, unless perhaps the article is up for approval. As this is a collaborative project, others might well indeed want to "meddle." If, as an editor, one disagrees with a change, one's option is to undo the changes (with an explanation why), not to prevent the possibility of changes in the first place. Cf.Statement of Fundamental Policies, section III.3.

Also, as to "didn't seem to be enough": the rules for approval are the same for everyone, and can be found at Approval Process. --Larry Sanger 19:31, 21 June 2007 (CDT)

I've removed Robert Tito's misplaced speedydelete template from the page, which is completely unjustified in this case, of course. --Larry Sanger 01:45, 22 June 2007 (CDT)

Approval status

I still feel myself a CZ newbie, especially with regard to the "approval process". I haven't seen an approval yet. Therefore I dare asking the following question: Would it make sense that I, being a chemistry editor, read this article carefully and give maybe some comments? Could it then be approved?

(There aren't definitely three chemistry editors willing to do it. As far as I can see it I'm the only active chemistry editor. So either approval has to wait until CZ has at least 3 active editors, or CZ has to make do with one editor, which in itself is already a huge improvement over WP).--Paul Wormer 11:43, 27 September 2007 (CDT)

Hey Paul, you will need to fill in the metadata template when you are ready to recommend this article for approval. See this example edit (except now should be a date, you can add with ~~~~~) i can look over the biology for you depending on how much you want to leave in the article. Chris Day (talk) 03:12, 28 September 2007 (CDT)

environmetal

Hi Robert, you caught me in the process of updatign and i redeleted the environmetal section. The other option is to move the whole lot down from the other section. Either way we should try and avoid the redundancy. Chris Day (talk) 14:01, 4 October 2007 (CDT)

Chris, The point is that the configuration is of no importance to this behavior (specific binding of multivalent heavy metals). It leads however to a drastic change in conformation: tightly packed precipitous balls. That has specific advantages in waste management - specially in polluted harbor silt.

For that reason I wanted it out of cofiguration - as it is no effect of configuration it merely is an effect of electrostatic interaction and the nearly infinite sulubility of PAA in water. Robert Tito |  Talk 

It's not in configuration, it's in the section about conformation that specifically points out that configuration is different. Isn't that an appropraite section? Chris Day (talk) 14:27, 4 October 2007 (CDT)

Khohlov-implosion

The following sentence at the bottom of macromolecules seems out of place.

DNA and other large biological molecules seem to use another mechanism similar to the so-called Khohlov-implosion of macromolecules, a kind of implosive diminishing of the size of the dissolved molecule where its hydrodynamic radius diminishes by a factor of 1000 or more. This implosion seems to be based upon specific environmental conditions based upon charge effects and low concentrations of (possibly) interfering other kinds of macromolecules."

I have a problem with this sentence since it is quite a general description of implosion yet uses DNA as an upfront example. I think it would be better to have a more general example. The DNA one seems too complex since it requires nucleosomes to actually achieve the compaction mentioned. I'm not familiar with the Khohlov-implosion so i'm not sure of other, better examples. Chris Day (talk) 14:48, 4 October 2007 (CDT)

Chris, a Khohlov implosion is an implosion of a partially charged macromolecule due to its statistical interaction with its environment. The result is that it's hydrodynamic radius decreases by a factor of 10000 and it's conformation into that of a tightly packed cigar, subsequently increasing the charge on the polyelectrolyte keeps the cigar shape more or less in tact but its radius increases again according to coulomb interaction. Robert Tito |  Talk  16:24, 4 October 2007 (CDT)

I understand what it describes, the explanation in the article is quite good. However, I have never heard of this term to describe the compaction of DNA, or any macromolecule for that matter. The use of implosion implies this is a spontaneous event and this is the wrong impression to give for the compaction of DNA leading to the formation of metaphase chromosomes. Even with nucleosomes present the compaction is not a final outcome. What are other non biological examples? Chris Day (talk) 21:20, 4 October 2007 (CDT)

Chris, one aspect is - but still under investigation the compacting of polyelectrolytes when interacting with heavy metals because the resulting product is nearly granular - more so then expected. I only used DNA as example to make it visualizable. There are soaps using this strange behavior as well, unilever being one of the labs involved. So that implosion (khohlov) is not directly correlated to the drastic compression of dna but it is involved as well. dna shows this compacting aided by nucleosome when the environment is suited for this super compression to occur and the conformation of dna is turned into elongated cigar shapes - much alike the resulting imploded polyelectrolytes (but then dna is that as well). Robert Tito |  Talk 

I was reading around and for a visual i wonder if the pearl necklace intermediate analogy would be more useful? I still think the DNA example, while majestic in its scale, is much more complex than the more simple compactions decribed by current research. There are just so many components to consider when looking at DNA. The PVP examples I saw are so much more simple.

I found a good example discussing protein folding which is better in my view because it is not relying on a host of other factors. I found that example at Protein Science (2002), 11:739-756. Natively unfolded proteins: A point where biology waits for physics by Vladimir N. Uversky He states "An intriguing property of intrinsically unstructured proteins is their capability to undergo disorder-to-order transition upon functioning. The degree of these structural rearrangements varies over a very wide range, from coil–premolten globule transitions to formation of rigid ordered structures." Chris Day (talk) 21:48, 4 October 2007 (CDT)

Chris, my point it - this article is not aimed at people with knowledge aboout the topic. I wonder if you mention that example to illustrate if anybody up from age 12 without knowledge of natural sciences can visualize what you try to explain. Based on didactics I seriously doubt it. I experimented a few times with people visiting open days at our labs and they even had a hard time imagining a loosely wound ball of wool expanding in water until I just showed them and dropped some loosely wounded wool in a bucket of water. Scientifically my example sucks, didactically it just does what it should do: be examplary. Any other reason why I used this example: none. People heard of this super coiling of DNA - something I gladly abuse to use as example. Robert Tito |  Talk 

True, but my point is that I know something about DNA but I got confused by your example. So you might not confuse a 12 year old since they know no better, but you will confuse people that understand the subject. This is why I was wondering if there is a better example that is accurate as well as being simple, if you see what I mean. Chris Day (talk) 22:15, 4 October 2007 (CDT)

By the way, is Khohlov-implosion a recognised term? It does not come up in literature searches. I was using searchs like "macromolecule compaction" to come up with the recent research in this area (like the review I referenced above). Chris Day (talk) 22:19, 4 October 2007 (CDT)

It was first observed at the Moscow University in the 1970's by Khohlov - hence its name. But I never ever found the article anywhere using the web, I do have a print out in russian and an awful translation in german. I do agree with your point Chris, it just is thats the best visualizer I see - maybe a small statement would suffice. Robert Tito |  Talk 

I'll think about it a bit more. It's a new concept for me, at least from the simple the synthetic macromolecule concept, so i need to let it sink in a bit. Is the important factor that the environment change? You mentioned heavy metals. What other types of factors can trigger implosion? Chris Day (talk) 22:41, 4 October 2007 (CDT)

I changed the text so it is obvious DNA is used as example for the implosion Robert Tito |  Talk 

Just noticed that, it's much better now. Chris Day (talk) 22:43, 4 October 2007 (CDT)

ok, this will be enough then - time to get the chemistry working not the what, in my user space I am starting a new article about just that. phys chem of macromolecules. Robert Tito |  Talk 

the important and needed factors are low charge, low concentration of the substance. A rigorous ∆charge will not reveal the implosion but only the result leaving you baffled about what happened and why. but I changed the text Robert Tito |  Talk 

Where's the chemistry

Despite the title, the article is maybe 10% chemistry and 90% descriptions and examples. As the article sits now, it should be named macromolecules, and have a subsequent page(s) detailing the chemistry. Pictures of alpha-helix and beta-sheet, simple DNA or RNA with phophate bonds, and some oil-based polymers would greatly aid the reader in understanding a monomer within a polymer. I also agree with the idea of having seperate pages for polymer chemistry, protein chemistry (synthesis of, enzymatic reactions of), DNA chemistry (synthesis of, oxidation of, methylation of, deaminiation, etc.) and so forth. Each of these topics would be huge all alone. The article is a nice description of the sorts of macromolecules that are known, but lacks chemistry. The section titled Physical polymer chemistry seems completely out of place in this article, and the first paragraphs of that section describe the nature of small hydrocarbons, not polymers.

All in all, I have been baffled by this page for quite some time and not sure what to recommend. David E. Volk 15:50, 4 October 2007 (CDT)

David, have you ever started an article about complex materials diving deep into the statistical physics and chemistry, the biophysical aspects, biochemical aspects and nt to forget the physical chemical aspects and science without explaining what the materials are? IMHO peopkle without any knowledge must be able to read and understand at least what it is the article talks about before explaining what it does and how it does what it does. For that reason I defined a more phenomenological approach: explain what things are and slowly delve deeper into the science. It is the way science is taught. You cant start with quantum mechanics when you dont understand one bit of physics.

A Khohlov implosion is an implosion based upon statistical physical phenomena due to the environment of a molecule. It was the main topic of my dissertation. People do know that DNA is super-compacted when inactive - you need no explanation to do there and as an example how this implosion might work and can ve visualized I used the DNA super-compacting. Once again: I have no intention to explain statistical physics, grafen theory, group theory or scaling theory in an overview. The examples used are chosen with care: they illustrate but need not necessarily be opponent of what you are using it for. Examples can be used for that purpose. As long as the model used shows what you want it to show. Robert Tito |  Talk  16:21, 4 October 2007 (CDT)

editor needed

I think the article is ready for approval, but as its main contributor I am not entitled to do that. Any takers? Robert Tito |  Talk  19:51, 4 October 2007 (CDT)

I think Paul was hoping to set it on the path towards approval? Chris Day (talk) 21:21, 4 October 2007 (CDT)

I am for half a year now actually Robert Tito |  Talk 

http://en.citizendium.org/wiki?title=Macromolecular_chemistry&direction=next&oldid=100181420