Revealed: Lipids are Sexist, Temporemental and Local Friday, Jul 1 2016 


 

When Baker et al. quietly published a gender-based difference in the concentration of lyso-phosphatidic acid (lyso-PA) in 2001 [1], it wasn’t taken all that seriously. This was partly because the methods they used for both isolating the lipid fraction and for profiling it were not conventional, and partly because it was quite a narrow result in the grander scheme of things. However, recent work by Sales et al. [2] might just be enough to broaden this observation. Sales et al. found that not only is there probably about a 10% natural variation in the lipid profile in healthy individuals, but that the profile of both lipids and fats is related to gender, the use of hormonal contraceptives and personal disposition.

Sales et al. report that there is a statistically significant difference in the blood plasma concentration of several lipids. This includes similar lyso-lipids to the lyso-PA targeted in the Baker study, but also larger fraction, mainstream lipids such as PC, PE, PI and sphingomyelin (SM) in healthy men and women in their 20s.

The differences between healthy women taking hormonal contraceptives and those who do not also appear to be significant, and they are also significantly different to the men. At first sight, the variation within each group is wider than the variation between groups, but student t-tests indicate that the likelihood of the difference in absolute values being down to chance is less than 5%, indicating a significant difference.

There is also evidence that the concentration of certain glycerides, including fats, is partly gender- and hormonal-contraceptive-dependent, with members of the latter group having higher triglyceride concentration than women who do not take hormonal contraceptives. This may have implications for treating illnesses related to lipoproteins, though further work is required to determine whether gender or hormonal contraceptives have a significant role in this.

This work is interesting enough on its own, but it comes shortly after another study, by Aviram et al., that showed that lipid distribution in certain parts of cells varies during the day [3] and a third, by Dawaliby et al. that showed that a lipid called PE is an important regulator of membrane fluidity in eukaryotic cells [4]. These studies between them show that the concentration of major structural lipids such as PE and PC vary throughout the day and are dependent on your gender and the pills you take.

These studies are juicy for lipid researchers because they support notions that lipid geeks like me have worked with for some time. For example, that the lipids we require for our cells to function are a dynamic and responsive group of molecules that we have yet to fully understand.

This work also raises a variety of questions. Are other factors important, like diet, temperature, the seasons etc.? What about the difference between the healthy systems studied and metabolic diseases? The list goes on. It also hints that lipids are under-rated parts of our cells that might be able to give away more information than we think.

References

1. D. L. Baker, D. M. Desiderio, D. D. Miller, B. Tolley and G. J. Tigyi, Analytical Biochemistry, 2001, 292, 287-295. 10.1006/abio.2001.5063.
2. S. Sales, J. Graessler, S. Ciucci, R. Al-Atrib, T. Vihervaara, K. Schuhmann, D. Kauhanen, M. Sysi-Aho, S. R. Bornstein, M. Bickle, C. V. Cannistraci, K. Ekroos and A. Shevchenko, Scientific Reports, 2016, 6, 27710. 10.1038/srep27710.
3. R. Aviram, G. Manella, N. Kopelman, A. Neufeld-Cohen, Z. Zwighaft, M. Elimelech, Y. Adamovich, M. Golik, C. Wang, X. Han and G. Asher, Molecular Cell, 2016, 62, 636-648. 10.1016/j.molcel.2016.04.002.
4. R. Dawaliby, C. Trubbia, C. Delporte, C. Noyon, J.-M. Ruysschaert, P. Van Antwerpen and C. Govaerts, Journal of Biological Chemistry, 2016, 291, 3658-3667. 10.1074/jbc.M115.706523.

 Banting Thin Friday, May 1 2015 


The broadest definition of lipids includes fats and cholesterol as well as biological amphiphiles. This means that the study of obesity is often regarded as part of the study of lipids. In fact, the study of obesity is a good broad definition of the clinical discipline of lipidology. The principal stuff of obesity is of course fat, referred to formally as triglycerides.

The structure of triglycerides give very little of their peripheral importance away: the social, emotional and even political meaning these molecules have is not at all evident from the molecules as we see them on the page. In fact, despite considerable research into human metabolism over the last hundred or more years, there has been very little impact on obesity. If anything, Europeans and North Americans are fatter now than they were a century and a half ago. This is despite the increase in our understanding of fats and the dangers they pose. This ‘obesity crisis’, if a crisis can happen as slowly as someone over-eating, also correlates with the popularisation of dieting.

In 1862, the undertaker by Royal appointment to the House of Hannover, a William Banting, published a ‘Letter on Corpulence: Addressed to the Public’. The document is still widely available, and makes interesting reading for social historians as well as lipidologists, and probably those interested in the psychology surrounding losing or gaining weight. It is about what became known as Banting, a form of dieting.

A look beyond the Victorian verbosity and veneration brings out familiar themes. He describes the perceived difficulties of corpulence—of being unfit, of having an awkward bodily shape, of lacking energy. He also fashions a superficially believable excuse for not increasing his calorific expenditure (taking more exercise), and hints at many of the ignorances of the time, including that fatness is age-related and that gout and obesity are linked.

Two particular things about this Letter stood out for me. First, that this appears to be an example of the belief that weight loss can, or should, or should only be attempted purely through dietary change. Second, that this is the first low carbohydrate diet, and forms the basis for all those that have been constructed in that vain since.

The idea that losing weight can be achieved through changes to diet alone is not necessarily wrong—no one who understood anything about human metabolism would tell you that it were—but equally there is no doubt that it is not the full story. The mass of triglycerides (amount of fat) in our adipose tissue can regarded rather like the amount of money in a bank account. If we spend more (take more exercise), the balance falls (we get thinner). If we earn more than we spend (eat more calories that are used), the balance goes up (our adipose tissue stores more fat). So, rather like running a current account, the balance between what is spent and what is earned is the key to changing the size of fat reserves. It is not just about what is earned.

Banting’s unwitting begattation of the ‘low carbohydrate diet’ is a bit harder to analyse. Certainly, he consumes fewer calories from starchy foods on his weight loss diet, to a level that he eats fewer than he needs and thus uses up his reserves. However, the diet also represents a considerable reduction in the intake of fat, and not necessarily as low a carbohydrate intake as one might imagine. He avoided pastry and fattier meats but also drank far more alcohol than is recommended today. The emergence of ‘low carb’ diets from this one is therefore a bit of a mystery. It was probably not widely understood in the 1860s was that fat contains more than twice as many calories as either protein or carbohydrate, gramme-for-gramme. Could it be that this is still poorly understood today?

Food is a complicated mixture of molecular species, and indeed the composition of foods is too complicated even to be at the centre of food science. Biochemical studies mean we now know that our omnivorous digestive systems and evolved metabolic machinery are well able to deal with a variety of molecular species. This means that we can tolerate a great variety in our diet. Our bodies can make fats out of both carbohydrate and protein, but cannot make either protein or carbohydrate out of fats. We can convert some protein monomers (amino acids) into others, and thus make up for a certain deficiency of amino acids in our diet, but by no means all—there are at least eight amino acids we must have in our dietary intake, the best sources of which are meats.

Human bodies are not really able to make carbohydrates at all–at least not ones for storing energy. Though we can get energy from fats, we rely upon carbohydrate absolutely. In fact, the basis of all terrestrial metabolism is the oxidation of glucose to carbon dioxide. Thus any organism that respites requires a supply of glucose. This means that although there is scope for a good deal of variety, the evidence is clear: there are some things we cannot expect to change.

However, the fact remains: no matter how clear the data, how good the science, or how thoroughly the fad diets and the bullshit of phrases like ‘low carbs’ are debunked, obesity remains. The science is not enough on its own, to stop the crisis. This suggests to me that the study of obesity is the study of the problem, more than the solution. Where the solution will come from is harder to say—but a hundred and fifty years of Banting has not yet given the answer.

References and Further Reading

Letter on Corpulence: Addressed to the Public, William Banting. (A simple google search will bring this up though links here, here and here work at the time of writing)

The Fats of Life, Caroline M. Pond. A dry and now somewhat dated but easy read on fats. More recent research includes evidence that illuminates our understanding of the genes involved in the metabolism of fats, see here.

 Hitting Your Head Against a Brick Saturday, Nov 1 2014 


 

An analogy of lipids I often use is that they are cellular bricks. They make up the membrane, the wall that separates the inside of the cell from the outside. So, this explanation gets across many of the facets of the lipid quite concisely—there are a variety of sorts, they do not work as individuals, when assembled together they form stable and often lasting structures that are usually much thinner than the spaces they enclose. The epithet ‘cellular bricks’ also suggests that, at least for individuals, they are not that exciting.

I make light of this by tackling the ennui head on, and use the word boring. This gets a half-laugh and gives my interlocutor the chance to say whatever is on their mind, usually either desperately thinking of something to say about anything else, or processing the idea that the word lipid is not synonymous with the word fat.

The trouble with this explanation is that it often leaves me feeling as though I have been pessimistic. There is no proper ‘lift’ at the end to leave things on a nice note.

I am pleased to say that recent work by Kuge et al. [1] and Ersoy et al. [2], has made me change my ideas about how I describe basic lipids—or at least reconsider my stand-up comedy explanation of them. These two reports show that one of the most common lipids in mammals and yeast, phosphatidylcholine, may be rather more exciting as a biological molecule than previously expected.

Kuge et al. [1] show that a particular type of PC, called 1-oleoyl-2-palmitoyl phosphatidylcholine, is concentrated at the tips of growing nerve cells. Ersoy et al. [2] report evidence that an enzyme called PC-transfer protein has a role in insulin signalling. Specifically, PC-transfer protein is involved in a part of the process that goes wrong in type II (obesity and gestational) diabetes.

These two things show a breadth in the functions of PC that are a considerable step forward in our understanding of this lipid.

Delving into it further, I found that there have been hints about this other life of PC for a while. The first evidence appears to be that PC can be a storage lipid. Specifically, it is a pantry for a kind of poly-unsaturated fatty acid called [3,4] that is itself a starting material for prostaglandins in inflammation pathways. Another nudge towards Bethlehem was the observation that it is used to make sphingolipids, lipids that are themselves important signals [5] (you can read more about the importance of sphingolipids here [6]).

The role of PC as a protagonist in the mechanisms behind cancer make it a worthy research interest. However, could one argue that the physical role of PC is more fundamental to our cells?

The first focussed biophysical work on lipids was done on PC in the 1960s. This early work was dominated by Vittorio Luzzatti, who published a paper in 1968 called ‘Polymorphism of Lipids’ [7], and much of it was done on PCs. It was shown that PC has a strong thermodynamic preference for forming bilayer sheets. This correlates almost exactly with how our cellular membranes are constructed. Cellular systems differ in that they have a gentle curvature, that is what allows them to be spheroid objects. In terms of bilayer geometry, this is easily accounted for, just have fewer PC molecules on the inside leaf. Added to which, there are other lipids present anyway. Several of the latter turned out to be lipids that induce curvature in membranes.

These two bodies of work, what we know about the physical behaviour of PC in forming membranes and its biological role in cancer and diabetes, are difficult to compare. It is almost the lipidology equivalent of fatuous questions about whether Newton or Shakespeare is better, or whether a sound exists if a person has not heard it.

The way I prefer to think about it is that the physical and biological importance of PC is like comparing the colour of an orange with its flavour. They are separate things, distinct aesthetic experiences. And one without the other is a bit spooky.

References

[1] H. Kuge, K. Akahori, K. I. Yagyu. Journal of Biological Chemistry, 2014, 289, 26783. doi: 10.1074/jbc.M114.571075

[2] B. A. Ersoy, A. Tarun, K. D’Aquino, N. J. Hancer, C. Ukomadu, M. F. White, T. Michel, B. D. Manning, D. E. Cohen. Science Signaling, 2013, 6, ra64. doi: 10.1126/scisignal.2004111

[3] V. A. Ziboh, J. T. Lord, Biochemical Journal, 1979, 184, 283.

[4] R. M. Kramer, D. Deykin, Journal of Biological Chemistry, 1983, 258, 13806.

[5] W. D. Marggraf, F. A. Anderer, Hoppe-Seylers Zeitschrift Fur Physiologische Chemie, 1974, 355, 803. doi: 10.1515/bchm2.1974.355.2.803

[6] B. Ogretmen, Y. A. Hannun, Nature Reviews Cancer, 2004, 4, 604. doi:10.1038/nrc1411

[7] V. Luzzati, A. Tardieu, T. Gulik-Krzywicki, Nature, 1968, 217, 1028. doi:10.1038/2171028a0.

 

 It All Flakes off When the Lipid Shortens Tuesday, Sep 30 2014 


 

The best word I can find for my reaction to a shoulderful of dandruff is off-putting. I have yet to meet anyone whom I know would disagree, including those who sport a pair of such shoulders themselves on a daily basis (if only they knew it). The only further thought I had had until now was an unkind one about whether or not those afflicted with this condition, use an anti-dandruff shampoo.

It is common knowledge that the white particles that we recognise as dandruff are flakes of scalp, i.e. the skin out of which our head-hair grows. The proper name for the condition is seborrheic dermatitis and it is something that affects 20% of humans of all ages. It is similar to what is called atopic dermatitis, a condition in which the non-scalp skin flakes off. It is often known as eczema. Atopic dermatitis affects 10-20% of children, but typically many fewer adults.

What I had never considered was what might cause the dandruff in the first place.

Recent research by Ishikawa et al. [1], Janssens et al. [2], Park et al. [3] and Tawada et al. [4], provide some clues. Taken together, these reports shows that the occurrence of atopic and seborrheic dermatitides correlate with a shift in the lipid profile of the skin. The evidence suggests that one lipid (with fatty acid residues that are 16 carbon atoms long, C16) is gained at the expense of one that is longer (24 carbon atoms long, C24). In other words, the hypothesis these data led to was that the fatty acids used to make these lipids are not made long enough.

In order to make sense of these observations scientifically, a recently-publsihed article by Skolova et al. [5] described the use of used a model system to research the physical impact of this change. This model was used whilst ensuring that the data generated were relevant to human skin (stratum corneum).

The model system they used consisted of the ceramide (either C16 or C24), a fatty acid (of typical chain length for mammalian lipid systems, C16) and cholesterol, also normally found in the stratum corneum. They determined the physical behaviour of the system in a comparable way using infra-red spectroscopy. This type of spectroscopy demonstrates how the fatty part of the lipid systems pack together. This technique can therefore be used to investigate the differences in packing between the C16 and C24 systems.

Both model systems behave a bit like ordinary bilayers, with the hydrophobic effect ensuring that bilayer-type systems are formed. However, the additional length of the C24 fatty acid residue in the ceramide may lead to several significant differences in the physical properties and parameters of the system. For example, the bilayer may thicken. Alternatively, the longer chain of the fatty acid residue might bend or even fold, to fill in gaps in curved systems.

In this system, which is typically rather drier than most naturally-occurring lipid systems, the effect is somewhat different. The evidence suggests that instead of a classical bilayer, the ceramide behaves more like a wax, in which the carbon chains are 180 degrees apart, rather than parallel (blue molecule, Figure). This means that the head group of the ceramide represents the hydrophilic part of the system—that which would normally be two faces of head groups and an aqueous fraction—and the system is held together as much by the van der Waal’s forces between hydrophobic moieties as it is by the hydrogen bonding and electrostatic (charge-based) forces.

Skin model and classical bilayer diagram
Figure. Left: diagram of the molecular assembly of ceramides, fatty acids and cholesterol in human skin. The blue molecules are not packed as classical lipids, but splayed at 180°, leaving the head group (blue ‘O’)in the middle, rather than on one face. Note how the hydrophilic parts of the cholesterol (red ‘o’) and fatty acid (black ‘o’) are assembled facing one another adjacent to that of the ceramide, forming an hydrophobic surface. (this diagram is from Skolova et al.[5], from data published by Iwai et al. [6]. Right: An ordinary bilayer. The structural parameter marked as ‘d-spacing is used to record the size and shape of systems.

It is therefore straightforward to realise how a much shorter chain—sorter by a third—might interfere with the balance of forces present in the system. We therefore expect that the skin that flakes to produce dandruff is rather weaker than normal and is the result of a faulty enzyme. The enzymes that produce longer-than-average-length fatty acids are called elongases.

Despite this insight, and how it has changed my view of what dandruff is, I must confess I cannot find use for it in conversation. Would anyone be able to say to someone with eczema “I’m sorry to see your elongases are not working at the moment”?

References

[1] J. Ishikawa, H. Narita, N. Kondo, M. Hotta, Y. Takagi, Y. Masukawa, T. Kitahara, Y. Takema, S. Koyano, S. Yamazaki, A. Hatamochi. Journal of Investigative Dermatology, 2010, 130, 2511−2514.

[2] M. Janssens, J. van Smeden, G. S. Gooris, W. Bras, G. Portale, P. J. Caspers, R. J. Vreeken, T. Hankemeier, S. Kezic, R. Wolterbeek, A. P. Lavrijsen , J. A. Bouwstra. Journal of Lipid Research, 2012, 53, 2755−2766.

[3] Y. H. Park, W. H. Jang, J. A. Seo, M. Park, T. R. Lee, Y. H.Park, D. K. Kim, K. M. Lim. Journal of Investigative Dermatology, 2012, 132, 476−479.

[4] C. Tawada, H. Kanoh, M. Nakamura, Y. Mizutani, T. Fujisawa, Y. Banno, M. Seishima/ Journal of Investigative Dermatology, 2014, 134, 712−718.

[5] B. Školová [Skolova], K. Hudská, P. Pullmannová, A. Kováčik, K. Palát, J. Roh, J. Fleddermann, I. Estrela-Lopis, K. Vávrová. Journal of Physical Chemistry B, 2014, 118, 10460 doi:10.1021/jp506407r

[6] I. Iwai, H. M. Han, L. den Hollander, S. Svensson, L. G. Öfverstedt, J. Anwar, J. Brewer, M. Bloksgaard, A. Laloeuf, D. Nosek, S. Masich, L. A. Bagatolli, U. Skoglund, Lars Norlén. Journal of Investigative Dermatology, 2012, 132, 2215–2225;. doi:10.1038/jid.2012.43.

 How Would You Explain Lipids to Someone Who Had Never Heard of Them? Saturday, Feb 1 2014 


 

When I want to explain my research to someone not from a science background, I normally opt to talk about it through a fundamental process that I am sure they will have heard of. Cell division is usually the best vehicle, and it segues nicely into a discussion about what I want to do in research in the long term if the conversation goes that far.

I start by explaining that we can draw an analogy between a cell and a house. If one were an alien and wanted to study houses, the things that move and go in and out of the house would probably be the first things that would gain one’s attention; the water, electricity, people and so on. However, I suggest, if you put the materials that allowed all of those things to happen together, a house would not emerge. A pile of pipes, windows, wires and so on is the contents of a skip and not Hampton Court Palace.

In terms of the raw material, the difference between the pile of stuff and the Tudor-Baroque masterpiece I mentioned can be summed up as the bricks. This is where I draw it back to lipids: they are a lot like bricks, I say. They are the bricks of the cell. Individually, they are unexciting and almost pointless. When put together in a coherent manner, great structures can emerge—everything, in fact, from a royal residence in Surrey, to a two-up-two-down in the east Midlands.

That is a neat explanation and usually satisfying, and that does not last longer than half a glass of merlot. Sometimes their interest goes further, and so I take the opportunity to push things up a notch; I take a slightly different approach. I explain that in terms of cells, we know a lot about DNA and how it behaves when cells divide. I mention Rosalind Franklin. Then I mention that proteins have been studied extensively and that we know that they make up some important molecular machinery of the cell. I mention that Nobel prizes have been won by British scientists for work on individual proteins in this story (Sir Tim Hunt and Sir Paul Nurse). Then comes the gap in our knowledge: the cell membrane.

Despite a great deal of research effort into cell division and related processes, like vesicle budding, I say that we know little about how membranes expand, bend and divide in living cells (in vivo). There is evidence about lipid behaviour from studies of model systems, and so we are confident of the basics. We understand about different types of lipid and the different sorts of assemblies they form. I also say that we know there are an amazing number of distinct lipids but we do not know how these might change in the process of cell division.

However, breaking news sheds light on the role of lipids in living systems. Some recent work by Atilla-Gokcumen et al. [1] has indicated that the concentration of certain lipids does change during the cell cycle. This exciting work, that became available to read in the journal Cell in January 2014, reports that eleven lipids with known chemical structures accumulate in dividing cells. This set includes phosphatidylinositol, several sphingolipids, phosphatidic acid, and a phosphatidylserine as well as two pseudo-lipids (a triglyceride and a sterol derivative).

This discovery shows that lipids may have a physical role in the process of cell division. This is a significant step forward; much of the evidence to date has been limited to model systems [2,3], has been theoretical discussion [4] or a best guess based on thermodynamics [5].

One of the reasons this discovery is important is that it is not an end in itself. Like virtually all good science, it opens up a multitude of options. It invites investigation of the behaviour and interactions of those lipids that increase in concentration in the run up to cell division. It begs the question of which lipids decrease in concentration during this process, and why. It invites fresh consideration of the evidence about those lipids that have been highlighted. It also invites interest in what changes to the lipid profile occur in other mammalian cells, and even in simpler organisms (I am working on bacteria at present, for example).

We have therefore had our appetite partly satiated and partly whetted, all at once. We have learnt a bit more about the physical process of cell division, with its connections to everything from cancer to the repair of a paper cut, and more fundamentally, that a class of molecules traditionally thought unexciting, may be on the brink of celebrity.

References

[1] G. E. Atilla-Gokcumen, E. Muro, J. Relat-Goberna, S. Sasse, A. Bedigian, M. L. Coughlin, S. Garcia-Manyes, U. S. Eggert, Cell, 2014, http://dx.doi.org/10.1016/j.cell.2013.12.015.

[2] X. Mulet, R. H. Templer, R. Woscholski and O. Ces, Langmuir, 2008, 24, 8443–8447. http://pubs.acs.org/doi/full/10.1021/la801114n.

[3] S. Furse, N. J. Brooks, A. M. Seddon, R. Woscholski, R. H. Templer, E. W. Tate, P. R. J. Gaffney, O. Ces. Soft Matter, 2012, 8, 3090-3093. DOI: http://dx.doi.org/10.1039/c2sm07358g.

[4] S. Furse, S. Liddell, C. A. Ortori, H. Williams, D. C. Neylon, D. J. Scott, D. A. Barrett, D. A. Gray. , Journal of Chemical Biology, 2013, 6, 63-76. DOI: 10.1007/s12154-012-0090-1 .

[5] H. T. McMahon, J. L. Gallop; Nature, 2005, 438, 590-596.

 Oxidative Stress on the Brain Saturday, Jun 1 2013 


Unsaturated fats are often regarded as healthier than their saturated equivalents. This translates into eating fish rather than beef burgers, chicken rather than pork and olive oil rather than butter or lard. These sorts of dietary changes have calorific advantages for those wishing to reduce their dietary intake of energy, as unsaturated fats contain slightly less energy than saturated fats.
Unsaturated fats are often described as having a number of health benefits, including reports in the popular press that they may ease type II diabetes and reduce heart disease. Although much of this evidence is not yet conclusive for the general population – with anecdotes about some sources of saturated fat sounding counter-intuitive at first sight – we do know a lot about the basic chemistry of unsaturated fat.
Anyone who has cooked with unsaturated fat (cooking oil) and left it exposed to the air for a period afterwards will be aware that the fat will become rancid – it rancidifies. Rancidification is a reaction between the unsaturated bonds in the oil and oxygen from the air; the unsaturated bonds are oxidised. This is what makes the flavour and smell of the fat much less attractive.
Unfortunately, this sensitivity to oxidation is inherent in unsaturated fats. In fact, the more unsaturated, the easier it is for them to rancidify. A further problem is that such fats do not need to be exposed to the air for oxidation to occur. Oxidation can also happen to fats in our bodies. Oxidation of fats in our cells happens much more slowly than in air, and happens when the fatty acid residues are attacked by oxygen radicals.

This phenomenon relating to the fatty acid residues in lipids in the eye has been discussed in this blog already, but there is mounting evidence that suggests oxidation of fatty acids and the metabolic products are important for normal metabolic function, but are also important in dysfunctional systems, including in the brain [1], in atherosclerosis [2] and in tissue repair [3].

If such a process is so widespread and influential, you may wonder why it has taken so long to come to light. The good news is that most life forms have evolved to be able to metabolise the oxidised fatty acids, removing them from the system. Recent research by Teixeira et al., [1] suggests that one method involves dietary intake of a specialised kind of fatty acid. This fatty acid contains what is called a furan ring (a five-membered ring comprising one oxygen atom, Fig. 1), but is otherwise not unusual.

F6 and a fatty acid

Fig.1, Top, Furan-containing fatty acid, known as F6; Bottom, eicosodienoic acid, an unmodified fatty acid that may be a precursor to F6.

Evidence from this study [1] suggests that once this modified fatty acid is in membranes, it is able to react with damaging oxygen species in the place of other fatty acids. This greater reactivity of the F6 is ascribed to its ability to ‘scavenge’ for the reactive oxygen species that would otherwise react with unsaturated fatty acids.

This mechanism is based on a replaceable molecule that suffers oxidative damage more readily than ordinary fatty acids. It therefore protects the others by acting as a sort of ‘fall guy’. How this mechanism operates allows us to draw a number of conclusions and ideas for future work. First, modified fatty acids such as F6 are present in fish oils and so dietary intake of seafood seems a good way of improving the availability of such molecular species. Second, an idea arising from the mechanism described by Teixeira et al., [1] is that it may be possible to prevent or reduce oxidation using chemical intervention. In other words, using this mechanism as a basis, it may be possible to develop treatments for conditions that result from oxidative stress. This has implications for how conditions such as Alzheimer’s and cardiovascular disease may be overcome.

References
[1] A. Teixeira, R. C. Cox, M. R. Egmond, Food and Function, 2013, in press, DOI: 10.1039/c3fo60094g.
[2] G. Spiteller, Ann. N.Y. Acad. Sci., 2005, 1043, 355. http://onlinelibrary.wiley.com/doi/10.1196/annals.1333.042/pdf
[3] E. Novo, M. Parola. Fibrogenesis & Tissue Repair, 2008, 1, 5. http://www.fibrogenesis.com/content/pdf/1755-1536-1-5.pdf

 

 Recycling Retinal Wednesday, May 2 2012 

‘Eating carrots makes you see in the dark’ is an commonly-used and fun way to encourage children to eat more in the way of vegetables. As we grow up, we realise that it does not really hold true because the problem with night-time is that there is no light, and no amount of dietary carrot can over come that. It is not until later that we may discover that there is a benefit in eating carrots. Specifically, that they provide vitamin A that our bodies use to make the photosensitive chemical, 11-cis-retinal, that we do need to be able to see.

Despite this, further exploration is needed to understand the chemistry of how components of a carrot can be used to produce a set of photosensitive systems capable of allowing us to read a set of traffic lights. Furthermore we lose and replace cells every moment of our lives, and there is no reason to think this would not apply to cells found in our retina, nor to the photosensitive chemicals found within them. This not only begs the question of how this part of our visual sense is made, but also how it is maintained over a period of several decades. By building on previous studies of 11-cis-retinal in eyesight [1-3], Maeda et al. [4] have started to answer these questions.

Retinal

Figure 1. 11-cis-retinal.

The evidence reported [1-4] suggests that damaged (i.e., worn-out) 11-cis-retinal is recycled in the retina. This is obviously a frugal and practical method for managing this system: animals that have long times between meals or are under famine conditions will suffer less damage to their vision than if they required it from every meal. This important adaptation allows predators to see prey and run after it, despite not having eaten for even several months (e.g., the crocodile), and also enables prey to see well enough to observe a predator and mount an escape. Moreover, many of the oxidation products of 11-cis-retinal in vivo are quite toxic to the visual system. Thus a fast and efficient system to minimise their presence is significant in retaining a working system.

However, the structure of 11-cis-retinal (Figure 1) presents a serious thermodynamic problem to this sort of recycling system in vivo. 11-cis-retinal does not dissolve in water or self-assemble and thus cannot be metabolised in a similar way to glucose or a lipid. So, two possible approaches to the problem are therefore either to make 11-cis-retinal soluble in water, or to make it self-assemble. The latter is basically the approach taken in biological systems, using a commonly found lipid, phosphatidylethanolamine (PE). A condensation reaction between 11-cis-retinal and PE produces a Schiff base (Figure 2) that ensures that the 11-cis-retinal is situated on the membrane’s surface and physically available for repair by cytosolic enzymes.

Figure 2. The condensation reaction between 11-cis-retinal (bottom left) and phosphatidylethanolamine (PE, top left) that is located on the inner surface of a membrane. The product of this reaction is known as a Schiff base (right). Typically, the retinal that forms the Schiff base will be partially oxidised, and thus in need of chemical modification to return it to functional 11-cis-retinal.

Though the placement of 11-cis-retinal on a membrane is important in reducing a thermodynamic barrier to recycling 11-cis-retinal, like all biological processes, it can go wrong. A certain type of age-related retinal degradation is well characterised. Sufferers are left in a dangerous position, physicians with a problem to solve, and drug companies with an entrepreneurial opportunity. The data from Maeda et al. [1] may contribute to improving the situation in which sufferers find themselves. A variety of drugs possessing a primary amine ( NH2) group, the same one as that in the PE that takes part on the condensation to give the Schiff base (Figure 2), have been tested. Drugs in general are typically chemically distinct because they can both dissolve in water but also pass through membranes. Thus a drug molecule with a primary amine group could both condense with 11-cis-retinal (in precisely the way that PE does) and remain in the aqueous phase. This would allow 11-cis-retinal to dissolve in the cytosol and be repaired in a system in which the lipid method for this did not work normally.

Data from Maeda et al. [1] suggests that there are several possible chemotherapies based on the concept of an amine-containing drug that can condense with 11-cis-retinal and thus make it soluble and available for recycling/degradation, however clinical trials have yet to take place.

References

[1] Y. Tsybovsky, R.S. Molday, K. Palczewski. Adv. Exp. Med. Biol., 2010, 703, 105–125.
[2] R.S. Molday, K. Zhang, Prog. Lipid. Res., 2010, 49, 476–492.
[3] M. Zhong, L.L. Molday, R.S. Molday, J. Biol. Chem., 2009, 284, 3640–3649.
[4] A. Maeda, M. Golczak, Y. Chen, K. Okano, H. Kohno, S. Shiose, K. Ishikawa, W. Harte, G. Palczewska, T. Maeda, K. Palczewski, Nature Chemical Biology, 2011, 8, 170-178. doi:10.1038/nchembio.759.

 

 

 Lipids Have Gone Quantum Dotty Thursday, Mar 1 2012 

When solving engineering problems, Leonardo da Vinci would often look to nature for inspiration.  Long after he died, and in the English speaking world, this sort of approach was Christened biomimetic problem solving.  It is used by engineers when designing the shape of aeroplanes [1] and by synthetic organic chemists in preparing compounds that appear in nature [2], as well as their analogues.

The inspiration for producing molecular tools for research or medical applications using nature as an example is still apparently rather novel.  A recent example of this is the use of Quantum Dots.  Although a term like quantum dots sounds rather fun, it tells us little about what they are or what they do.  That they are, is a small amount (dot) of a compound not found in nature, that is surrounded to a particular type of amphiphile (lipid) that has been designed so intricately that it hardly bears comparison with naturally-occurring lipids.  This means the QD is rather like the micelles seen in soap, but with an inorganic compound in the centre.  What quantum dots (often known as QDs) do, is respond to particular wavelengths of light in a way that none of the rest of the material in the cell does. This makes them very clear and thus easy to detect.

Figure 1. Examples of amphiphiles that are used to surround fluorescently-active quantum dots [3]. These dots fluoresce at 535 nm and are relatively stable in biological systems as they are relatively small with respect to other quantum dots. The head group part of the amphiphilic section is similar to that in phosphatidylcholine. The end of the lipophilic end is bonded covalently to the quantum dot, and it is this interaction that is often damaged, leading to destruction of the dot.

Figure 1 shows some examples of quantum dots from a recent paper in Nature Chemistry [3] that documents research into the use of quantum dots as imaging tools.  The compound used for the dot, cadmium selenide (CdSe, sometimes doped with zinc sulphide, ZnS [3]), is utterly unknown in natural biological systems and perhaps for this reason the components are carcinogenic and require all sorts of precautions during use.  However, the lipid mono-layer covering of the CdSe means that Zhu et al. and many others have been able to use quantum dots for imaging in live cells [3].  The quantum dot itself is both sufficiently different from its surroundings and fluorescent enough to be used to detect very small numbers of cells.  However, the compound in itself requires protection in order to have specificity in biological systems.  A mono-layer of synthetic lipids is used to provide a barrier between the toxic compound and the aqueous system in which it is suspended.  The self-assembly properties of lipids mean that the system can remain intact under physiological conditions, and thus be transported through bilayers and between membrane compartments [3].

The fact that such quantum dots can be stabilised through the use of specially designed lipids increases their stability to a point that means that we can gain a sharper insight into a variety of processes in live cells.  The dots shown above last longer and so the relative intensity of the fluorescence can be used to indicate concentration of the dots with respect to the amount put into the system.  Studies to date have found that these markers can be used to track enzyme activity [4], which has applications in detecting given diseases.  Perhaps more fundamentally, quantum dots can be used to look at cells during gene expression, and thus track whether particular proteins are being made, and thus provide evidence for genetically-determined disease [5].  If this is the capability with current technologies, what will we see with improved stability and specificity?  The future of quantum dots is not just bright, it is fluorescent.

References

[1] “Airbus presents a panoramic view of 2050” http://www.airbus.com/newsevents/news-events-single/detail/airbus-presents-a-panoramic-view-of-2050/
[2] Helen C. Hailes, Ralph A. Raphael, James Staunton, Tetrahedron Letters, 1993, 34, 5313-5316. http://www.sciencedirect.com/science/article/pii/S0040403900739839
[3] Zheng-Jiang Zhu,Yi-Cheun Yeh, Rui Tang, Bo Yan, Joshua Tamayo, Richard W. Vachet, Vincent M. Rotello, Nature Chemistry, 2011, 3, 963-968.
[4] Stuart B. Lowe, John A. G. Dick, Bruce E. Cohen, Molly M. Stevens, ACS Nano, 2012, 6, 851–857.
[5] James E. Ghadiali, Stuart B. Lowe, and Molly M. Stevens, Angewantde Chemie International Edition, 2011, 50, 3417 –3420.

 Fat is a Biological Issue Saturday, Feb 18 2012 

One of the first things we may notice when we meet someone new is whether they are fat or thin.  Equally, one of the first things we notice about people we know, but may not have seen for some time, is whether they have gained, or lost, weight.  The fact that the mass of adipose tissue can differ within an individual, and indeed fluctuate in their lifetime, is perhaps a clue to how our bodies store fats.

It is correctly well known that fats are a biological energy store.  In mammals, fats are stored in cells called adipocytes.  It is a useful adaptation to be able to store energy for use later, as it means that meals can be further apart and larger, if necessary.  Some species are much better at this than us, as demonstrated recently on a BBC documentary by Prof Richard Fortey.  Some species of turtle, and crocodiles, can survive for well over six months without a meal.  Indeed, this is an important factor in how their species survived a mass extinction event 65 million years ago in which their previous sources of food were compromised.  The ability of such cold-blooded creatures to reduce their calorific expenditure, by lowering their body temperature, is also a factor.  Although warm-blooded mammals such as humans would be hard-pushed to survive such an event if it happened today, we have at least adapted such that typically, missing a meal or even two, does not result in death due to starvation.

These observations beg questions about how fat is stored in our bodies, how it is stored in the bodies of metabolically efficient reptiles like crocodiles, and how our bodies release these stores of energy.  It would be no good if the stored energy were unavailable at the crucial moment.  Equally when the energy is released, it needs to be the right amount such that the individual can do what it needs to, without wasting those stores.

Mammals differ from plants in how fat is stored: in mammals there is one large fat droplet per adipocyte, whereas plants tend to use several, smaller stores. Adipocytes can be up to 120 µm wide, roughly 15 times wider than a sperm cell (8 µm) [1].  This enables them to store large amounts of fat in each cell.  This is part of the reason why, under normal circumstances, the number of adipocytes in a person does not change.  What changes if they gain or lose weight is the size of the fat store in each cell. The operation that removes some of the fat cells is called liposuction.

The vehicle for this storage of energy is the triglyceride (Figure 1).  Interestingly, this is exactly the same molecule used by plants for the storage of fat, and is the principal constituent of olive oil.  Triglycerides are moved around our bodies by assemblies called lipoproteins.  This means that when muscular tissue requires energy from fat stores, it can call upon that stored in adipose tissue, similar to the way that you can order your food shopping on-line and have it delivered to your house.

Once the fat arrives at the cells that will metabolise it, such as muscle or liver cells, the lipoproteins are taken up by the cells and place the fat in small reserves in the cell [2].  These are not convenient for long-term storage in muscle cells in particular, and so the vesicle that contains the lipoprotein is soon joined by another organelle called a lysosome.  This organelle provides the enzymes required for metabolising the proteins delivered, while the triglycerides are given over to mitochondria.  Mitochondria are responsible for turning the fat into energy and it is thus not for nothing that they are known as the power-houses of the cell.

Figure 1. Triglyceride, a molecule composed of three fatty acid molecules and one glycerol moiety. The blue sections represent the lipophilic part of this pseudo-lipid, where the red section is the most polar part of it. However, this polarity is insufficient to confer self-assembly properties on the molecule and thus it is a fat, rather than a lipid.

The chemical process goes by the unlikely-sounding Citric Acid Cycle (CAC), the discovery of which won Sir Hans Krebs a Nobel Prize in 1953.

You may be wondering where the atoms that made up the fats go.  Needless to say they are not destroyed by our bodies, so they must be dealt with somehow.  Figure 1 shows that fats are made up of carbon, hydrogen and a little bit of oxygen.  The hydrogen binds to oxygen, forming water that can either be lost in urine, or more usually, as water vapour in our breath*.  This is only part of the reason that heavier breathing is typical during physical exertion; the carbon from fats is turned into carbon dioxide that is also lost when we breathe out.

One last point about fats is that, like cholesterol, we can make as much of it as we need to.  Thus the nutritional requirement for fat is virtually nought, though they do have an impact on our enjoyment of a meal.  This adaptation indicates to biologists that a varied and not necessarily regular dietary intake was a significant factor at some point in human evolution: we have adapted to enjoy eating fats but can make all we need.

References and Further Reading

[1] B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, P. Walter, Molecular Biology of the Cell, Garland publishing, 3rd edition, 0815316208.

[2] D. Voet, J. G. Voet, C. W. Pratt, Fundamentals of Biochemistry, John Wiley, 0471586201.

*We lose around 0•1 mL of water each time we breathe out. Based on breathing out once every 3 seconds, this means we breathe out just under 3 L of water each day.  Three or four urinations per day, of around 200 mL each, give rise to the loss of less than 1 L of water/day.

 

 Lipids – Where Do I Go? Thursday, Feb 2 2012 

Research is a notoriously vague occupation. It has more in common with gathering than hunting, and so inevitably has as much support as opposition. Researchers of all types will probably tell you that there is no substitute for putting the hours in and, of course, knowing where and how to look. These skills are undoubtedly useful when wanting to find more information on a subject as wide as lipids. In researching something in the 21st Century, our first port of call is typically Google, or, when in dire straits, an on-line encyclopaedia that is best left unnamed. As a source of information on lipids I cannot speak highly enough of this blog of course, but even it cannot contain everything. So, what if you need to go further?

There is a huge wealth of what is known as primary literature. These are original research papers that have been published in peer-reviewed journals*. What this means is that a scientist, or more usually a group of scientists, has written up some experimental work typically in a format of several sides of A4 long. This is submitted to a scientific journal, who send it to anonymous reviewers, who then send back comments. Assuming that the reviewers are not out of their depth, and the authors are professional about the process, the manuscript will be modified by the authors and resubmitted. If it is then thought suitable, it is accepted for publication. A large number of articles are accepted every month, these are published in sets (issues). As one may imagine issues are bound together to make up volumes.

The wealth of information in the primary literature is undoubtedly a hugely important one. It is often not necessarily difficult to find journals that are focussed on lipids; indeed there are a number focussed in this area, but there are some limits to this source of information. Unfortunately, such journals can be difficult to obtain access to if readers are not members of subscribing institutions (Universities etc.). Additionally, finding the right papers can be difficult for non-specialists: it is as easy to get bogged down as it is to miss crucial works. A more readily accessed, and smaller body of work, is the secondary literature.

Secondary literature is the term commonly used to refer to books on a given subject. A quick search on Amazon readily reveals the abundance of lipid literature that is available. Inevitably some titles can be picked up for almost nothing, a nominal £0.01 plus postage, and can allow one to put together a library of sorts on this subject with little effort. Although they are mostly titles resulting from investigative analyses of fat or lipid components of food – trans fats, cholesterol and so on – they provide a source of practical information. Others are perhaps a bit less scientific – for example, some seek to draw a distinction between good and bad fat, and another that appears to purport the belief that lipids form an important part of slowing the ageing process.

There is much in the mid-range but if you are feeling rather rich, educational and scientific books about lipids with much smaller print runs, but much more reliable information, are also available. At current prices, a little over £800 can buy you a copy of Lipid Research Methodology from 1984. Although now probably superseded in all principle tenements, it provides a good historical view of lipid chemistry. A newer book for a mere snip over £900 is The Chemistry of Oils and Fats. If you feel you have more spare money than can be sated by even those, around £1,700 can buy you a treatise on lipid microbiology and for a little more than £3,000 a thorough guide to the mass spectra of lipids is available (!).

You may be comforted to know that few lipid chemists have any such titles, either in the laboratory, or at home. Larger scientific reference libraries may do better, but as the subject of lipids is wide, taking in aspects of biology, chemistry and physics at least, you may prefer to find the right person to ask, instead. And you will be pleased to hear that Google is as good for that as anything else.

 

*Although non-peer reviewed journals are available, these typically have little value in scientific circles as the work published is not subjected to the rigorous scrutiny afforded by peer-reviewed journals to their issues.

 Biological Signalling Thursday, Dec 22 2011 

The approach of determining the lipid composition of living systems, called lipidomics [1], has demonstrated that a huge number of lipids are present in living systems.  Recent publications showing this in sharp focus include reports of the complete lipidome of part of the murine (mouse) immune system [2] and human plasma [3].  What this work shows, is that there are over 500 distinct molecular species distributed amongst the established lipid categories.  Reasoning would suggest that this is a large number of lipid types for the physical job of producing a cellular membrane (despite the need for several types of lipid in order produce a cellular membrane).

This begs the question: what are the remaining lipids for?  It is tempting to believe they have no function, however evolution suggests that this possibility is unlikely in nature, i.e., what evolutionary advantage would there be to produce lipids that are of no use?  What is far more likely is that there is a function.  And indeed this turns out to be the case.

Several of the minor lipid components of these systems are known to be biological signals.  Inositides are the dominant example of this.  One member of this group, called PIP3, forms part of the system that manages the release of insulin from the β-cells of the islets of Langerhans [4].  However, there is also much evidence [5] that PIP3 is also involved in the activation of a protein called PKB.  This protein is an enzyme that phosphorylates other proteins, activating them.  Enzymes that phosphorylate are called kinases, hence PKB: Protein Kinase B.  This enzyme, or more specifically, the phosphorylation it performs, is at the heart of the body’s control of growth.  It is therefore similar to the sort of signalling systems that go wrong in diseases such as cancer.

The research into PIP3 has been seen as important, and the development of an understanding arising from them, significant. This lipid has even been prepared using synthetic organic chemistry [6], such that sufficient stock of this lipid is available for further research. However, the fact that this lipid has proved to be so important in biological systems has made the other seven inositides rather more attractive than they once were. Thus, attention is now turning towards them. Phosphatidylinositol itself is the precursor to all other inositides. Kinase activity similar to that elicited by PKB turns phosphatidylinositol into inositides such as the phosphatidylinositol phosphates. There are three types of phosphatidylinositoldiphosphate head group, but only one phosphatidylinositoltriphosphate. Although no signalling role has been discovered for phosphatidylinositol, what has been discovered is that it can have a pronounced effect on the curvature of the lipid system of which it is part [7].

The demonstration of a pronounced effect on membrane curvature and an important biological signalling role for lipids that are closely related chemically is a bewildering thought. Are inositides an unappreciated force in vivo?

References

[1] E. A. Dennis, Proceedings of the National Academy of Sciences, 2009, 106, 2089–2090. http://www.pnas.org/content/106/7/2089.full.pdf+html?sid=e68904de-d625-41e0-aa17-cc9a36be94c2

[2] E. A. Dennis, R. A. Deems, R. Harkewicz, O. Quehenberger, H. A. Brown, S. B. Milne, D. S. Myers, C. K. Glass, G. Hardiman, D. Reichart, A. H. Merrill, M. C. Sullards, E. Wang, R. C. Murphy, C. R. H. Raetz, T. A. Garrett, Z. Guan, A. C. Ryan, D. W. Russell, J. G. McDonald, B. M. Thompson, W. A. Shaw, M. Sud, Y. Zhao, S. Gupta, M. R. Maurya, E. Fahy, and S. Subramaniam, Journal of Biological Chemistry, 2010, 285, 39976-39985. http://www.jbc.org/content/285/51/39976.full.pdf+html?sid=1a75f1d7-9661-4fc8-af76-cd29dd1cc326.

[3] O. Quehenberger, A. M. Armando, A. H. Brown, S. B. Milne, D. S. Myers, A. H. Merrill, S. Bandyopadhyay, K. N. Jones, S. Kelly, R. L. Shaner, C. M. Sullards, E. Wang, R. C. Murphy, R. M. Barkley, T. J. Leiker, C. R. H. Raetz, Z. Guan, G. M. Laird, D. A. Six, D. W. Russell, J. G. McDonald, S. Subramaniam, E. Fahy, and E. A. Dennis, Journal of Lipid Research, 2010, 51, 3299-3305. http://www.jlr.org/content/51/11/3299.full.pdf+html?sid=a1eb540d-d814-47ad-b102-455aeb3852b2

[4] O. I. Hagren and A. Tengholm, Journal of Biological Chemistry, 2006, 281, 39121-39127. http://www.jbc.org/cgi/doi/10.1074/jbc.M607445200

[5] B. A. Hemmings, Science, 1997, 277, 534. http://www.sciencemag.org/content/277/5325/534.full

[6] P. R. J. Gaffney and C. B. Reece, Journal of the Chemical Society, Perkin Transactions 1, 2001, 192-205. http://pubs.rsc.org/en/content/articlelanding/2001/p1/b007267m

[7] X. Mulet, R. H. Templer, R. Woscholski and O. Ces, Langmuir, 2008, 24, 8443–8447. http://pubs.acs.org/doi/full/10.1021/la801114n.

 Lipidomics Thursday, Dec 15 2011 

One of the big questions in biology is how living organisms work. How do we stay alive?  Understanding of this over the last two centuries has led to the development of science into the chemistry that sustains life in biological systems.  This is what biochemistry is.  A recent approach to understanding living systems has been to work out what all the genes are in a given organism.  This is all the genome is: all the genes an organism possesses.  Knowing what the genes are is useful because it tells us which proteins can be made. These proteins go on to do a variety of things, like speeding up digestion (enzymes), or for making the machinery required for cells to control what passes through their membrane (e.g. ion channels, which you may have read about here).  Genes and cataloguing the genome is an important advance in science, but it does not tell us everything. 

It is also useful to understand the range of other components present in a system, such as the lipids.  Knowing the complete lipid profile, the lipidome, of a system is particularly informative.  The word lipidome may seem unfamiliar, but it is the lipid equivalent of the genome in genetics, that is, a catalogue of every lipid in a given species. 

Once we know which lipids are present, and how much, we can use published evidence of the individuals’ behaviour to make conclusions about the relationship between what we observe in vivo.  Physical evidence from biophysical studies, such as the use of x-rays to determine the topology of the self-assembly in lipid systems [2], is also used to inform the understanding of these systems.  Lipidomics [1] is a relatively new approach to understanding the lipid fraction of biological systems.  In physical terms, it allows us to re-construct the system from the known behaviour of its parts. This is a more fundamental approach that is perhaps superior than simply doing things to lipid systems to find out what happens, such as adding chemicals that disturb the forces that hold lipid systems together.  Such chemicals are celled chaotropes [3,4,5]. 

Lipidomics sounds remarkably easy. We know what we need to do, and there are just a couple of steps to achieve it. We have a problem, however. Isolating these lipid molecules is more difficult than for proteins or DNA. Certainly adding solvents to dissolve the lipids makes sense, but this is awkward if we consider the relationship lipids have with water, and particularly so if they are more like a surfactant (i.e. soap) than a lipid.  This has not stopped tenacious lipid chemists from using sophisticated solvent systems to extract lipid fractions from plant, animal, or fungal material [6], however.  But this on its own is not enough.  Current lipidomics methodology also uses mass spectrometry to identify the molecules according to their molecular mass.  If this is accurate enough, it can be used to determine the number and identity of the atoms present.  This in turn is used to pin down the lipids’ identity. 

If this approach is applied to a whole organism, such as Saccharomyces cerevisae [6], the species of yeast used in baking bread and making beer, the results produce a lipidome of that species.

The lipidome tells us about the range of lipids the system is capable of producing, and does produce, which then informs us about the range of physical behaviour of membranes in the system.  The most exciting thing about this, in my opinion, is that we might then be able to understand the role of lipids in cell division.  How we get from one cell membrane to two is a physical process, but without an understanding of the lipid component we cannot construct a picture of how this happens on a molecular level.  Once we do, the understanding of lipids in a system will be at the same level as that of DNA and proteins.

References

[1] M. R. Wenk, Nature Reviews, 2005, 594, 594-610. http://staff.washington.edu/mwhiddon/Wenk%20et%20al.pdf
[2] X. Mulet, R. H. Templer, R. Woscholski, O. Ces, Langmuir, 2008, 24 , 8443–8447. http://pubs.acs.org/doi/abs/10.1021/la801114n
[3] K. Kinoshita, M. Yamazaki, Biochimica et Biophysica Acta, 1997, 1330, 199-206.
[4] G. C. Shearman, S. Ugazio, L. Soubiran, J. Hubbard, O. Ces, J. M. Seddon, and R. H. Templer, Journal of Physical Chemistry B , 2009, 113, 1948–1953. http://pubs.acs.org/doi/abs/10.1021/jp807998d
[5] Y. Feng, Z. W. Yu, P. J. Quinn, Chemistry and Physics of Lipids ,
2002, 114, 149–157. http://www.kcl.ac.uk/kis/schools/life_sciences/life_sci/quinn/publications/cpl114.pdf
[6] C. S. Ejsing, J. L. Sampaio, V. Surendranath, E. Duchoslav, K. Ekroos, R. W. Klemm, K. Simons and A. Shevchenko, Proceedings of the National Academy of Sciences, 2009, 106, 2136-2141. http://www.pnas.org/content/early/2009/01/27/0811700106 .

 Curvy Biology Friday, Dec 9 2011 


There is no such thing as a straight line in nature. This is especially obvious in cells and in their membranes. The absence of straightness from biological systems, including that of bilayers, presents a problem for membrane biophysicists and lipid chemists. Although the principles governing the way the lipid molecules used by cells to make membranes are well understood for flat bilayers, the presence of curvature provides an additional dimension to what we see. However, as with a lot of science, it gets a little bit more complicated before it gets simpler.


Figure 1. Curvature in membranes. (a) Prostate cancer cell, taken by Robyn Schlicher of Georgia Institute of Technology, showing normal curvature of all membranes; (b) A bilayer of phosphatidylcholine, showing that this lipid cannot form a curved surface as this would require vacuums in between the lipids; (c) The inclusion of cone-shaped lipids into a PC bilayer allows the layers to produce a curved surface without a vacuum.


Figure 2. Curvature in membranes arises through lipids of differing shapes. Left is the type II phosphatidylethanolamine, that gives rise to negative curvature. In the middle is the type 0, cylindrical, phosphatidylcholine that does not induce any curvature. On the right is lyso-phosphatidylcholine that brings about positive curvature in membranes.

The bilayer of lipids that makes up the plasma membrane is constructed of two mono-layers that face in opposing directions. Thus in order for the bilayer to bend, the mono-layers must bend in opposite directions in order that the bilayer bends as one entity and does not form a vacuum in between the mono-layers (Figure 1a). Mathematicians will say immediately that this means the leaf on the inside of the bend* has a smaller surface area. So, with a smaller surface area, why does the cell not have fewer lipids on the inside than on the outside? The answer is that it does, but that this is not enough to bring about curvature on its own, as there would still be gaps (Figure 1b). This problem is solved by the cell having lipids that are of different shapes (Figure 1c).

We are familiar with lipids that produce flat bilayers, such as the phosphatidylcholines, including Dioleoylphosphatidylcholine (DOPC). These are called type 0 lipids. There are also type I lipids, and type II lipids (Figure 2). Type I lipids include a modified form of DOPC, in which one of the fatty acid residues has been removed. This is known as lyso-PC. This is type I rather than type 0 because the choline head group is larger than the greasy hydrocarbon fraction, and so the lipid forms a cone shape. This cone shape means the lipid’s presence in a bilayer encourages positive curvature – curvature away from the water. This is useful to the spheroid cell, as the outside of its membrane can curve away from the water. This is complimented by type II lipids, in which the fatty acid part of the lipid molecule is wider than the head group. As we cannot bolt another fatty acid residue onto PC to make it type II, we can instead modify the head group to make it smaller. This gives rise to an entirely different type of lipid, called phosphatidylethanolamine.

So, with just these three lipids, we can bend a lipid monolayer in either direction. If they were arranged around something, they could even form a textured, or curvy, surface. Mitochondria, the powerhouses of the cell, need a large membrane inside as this is the surface required for many of their chemical reactions to take place. This inner membrane requires the presence of all three of these types of lipid in order to bend into flaps to give itself this large surface area (Figure 3). This, however, is not the full story. Although further work has been done, exactly how the membrane changes and its dynamic nature through processes such as cell division are not yet fully understood.     


Figure 3. Curvature in membranes in the mitochondrion; , shown in both an electron micrograph, and a drawn diagram. Image from Brooklyn College City University of New York
 


Notes

* In in a cellular system, bending towards the water is known conventionally as negative curvature.

 What Do Membranes Do? Thursday, Nov 24 2011 


We know that membranes in cells are complicated, and we have a pretty good idea of what they look like (Figure 1). We also know that the plasma membrane, the membrane that is the edge of the cell, is the thing that makes the cell a cell. At the very least, it means the cell is a discrete entity, and not just a loose collection of cell parts in one place. This might seem a serious job on its own, and it is, but there is more.


Figure 1. Schematic representation of a cell’s plasma membrane, showing the lipids along with peripheral and integral proteins, glycoproteins, surface proteins, ion channels, and carbohydrates. Note also the cytoskeleton filaments that, together with the plasma membrane of the cell, give it a life-supporting structure. Picture courtesy of WikimediaCommons.

Figure 2. Schematic representation of vesicles, with lipids forming a bilayer around a small body of water with other solutes (green blobs). Picture courtesy of WikimediaCommons.

Bilayers, such as that shown in Figure 1 contain various types of protein and some bits of carbohydrate*. However, to do the job of separating the cell’s insides from its environment, none of these other components are necessary. It is perfectly possible to create a sturdy bilayer from lipids alone. When this bilayer is formed in flat sheets and stacked up four-by-two, it is known as a lamellar phase [1], and when a bilayer is shaped like a ‘bubble’, it is known as a vesicle (Figure 2) [2].  Vesicles may sound a curiosity, but they are very useful in research laboratories. They provide a sort of stepping-stone to understanding complete cells as they can be of a similar size, but are much less complicated biochemically. So, if a scientist wants to test an idea or hypothesis without the complications of a testing it on a whole cell, a vesicular system is a useful one to try it on first. If the job of being a skin, a border between the inside of the cell and the outside, can be done so simply by a lipid bilayer, why does the cell go to the trouble of having the rest of the gubbins there?

The question becomes more pressing when we consider that there are a variety of proteins in the membranes of cells of both animals and plants. Not only that but, proteins are oten more complicated to make than lipids. The question has been raised not only about cells, but also about the parts of a cell that have a membrane or mono-layer covering of lipids. These parts of a cell are known as organelles.

Murphy and Cummins [3] asked this question directly about the organelles that store oil in seeds like Brassica Napa (rape seed). It is an interesting question, and there is an understood answer.   Consider this: if you were to put together an organisation of people in order to produce, say, a new range of chocolates, you would undoubtedly want several types of person. You would want people who could physically make the chocolate itself, so that you had chocolate to sell; you would want people who could design the chocolates, so the product had a chance of being consistent, coherent and tasting good; you would want managers to over-see the work of both of these teams; you would want market analysts, a legal team, HR and so on. Many types of people, probably too tedious to name individually. But you would need something else, too. You would want them to be able to talk to one another. You, as the philanthropist of your very own chocolate–making enterprise, would need them to communicate so the company’s activity is co-ordinated and coherent. With cells, it is just the same: the various organelles need to be able to communicate with one another in order that the cell can stay alive.   In order for a cell to stay alive, it must do a multitude of things – take in food, get rid of waste, resist changes in the environment, grow and replicate, to name but a few. And of course all of this must be co-ordinated so the cell does not die. An important part of this is cellular signalling.

As you might imagine, in order to perform a complicated set of processes, cellular signalling takes on a variety of forms – just like the large vocabulary required for a whole company to communicate with itself effectively. The complexity of cellular signalling has been made clear in recent decades, and now there are at least four scientific journals that focus on this aspect of biology alone, namely Cellular Signalling, the Journal of Cell Communication and Signalling, the Journal of Molecular Signalling, and Cell Signalling Biology.   The role of lipids in cellular signalling is a wide topic, and will be examined in other entries in this blog. Examples include how insulin lowers blood sugar level, and how the cytoskeleton (Figure 1), and thus the shape of the cell, is managed.

 

References and Notes

*Anything with the prefix ‘glyco-’ either is a carbohydrate or has one attached to it.

[1] F. D. Gunstone, John L. Harwood, Fred B. Padley, The Lipid Handbook, 2nd Ed, 1994, ISBN-13: 978-0412433207.

[2] J. C. Stachowiak, D. L. Richmond, T. H. Li, F. Brochard-Wyart, D. A. Fletcher, Lab on a Chip, 2009, 9, 2003–2009.

[3] D. J. Murphy, I. Cummins, Phytochemistry, 1989, 28, 2063-2069. http://www.sciencedirect.com/science/article/pii/S0031942200979214

 What is a Lipid? Tuesday, Oct 25 2011 

For most people who have heard it, the word lipid sounds like the scientific word for fat. Although scientists tend not to use the word fat, and do tend to use the word lipid, the two do not quite match-up. When we say fat in the context of food, we think of cooking or olive oil, butter, grease and possibly cream. Perhaps confusingly, all of these have lipids in them, but none of them are pure lipids.

The confusion about these strange molecules is probably related to the fact that they are hard to pin down. There is virtually an art form in isolating them. Only in the last 50 years have we really started to understand them, or their role in biology. The thing that makes lipids what they are, is that they are what is known as amphiphilic. This is from the Greek ‘amphi-‘, meaning ‘both’, and ‘‑philic’, meaning ‘loving’. Although this sounds like an intellectual’s way of referring to a bisexual person, here the ‘both’ refers to water and grease. As we know, water and grease do not mix: if we pour oil onto water, the two just sit there. Lipids are special because they can dissolve in both of them. This property can even be used as a way of mixing grease and water together. Homogenous mixtures of grease and water with another agent are known as emulsions. Examples include milk, cake batter and margarine. The emulsion as a construct is useful in the manufacture of foods, giving rise to a plethora of agents that are able to perform this role, namely emulsifiers. Although in theory all lipids can be emulsifiers, not emulsifiers all are lipids.

We can see the roots of the amphiphilic behaviour in the structure of the lipid molecules. Moreover, structural analysis of molecules can help us determine whether or not a molecule is a lipid at all, and if so, which sort. Figure 1 shows an ordinary lipid with the head (water-loving) and tail (grease-loving) regions marked out.

Figure 1.  Phosphatidylcholine (Lecithin). The red section represents the hydrophilic (water-loving) section, whereas the blue represents the greasy-loving section.

The structural approach has been used by several institutions in recent years, including Lipid Maps.  This has given rise to a broader definition of the term lipid.  Thus, a variety of compounds not traditionally referred to as lipids are included, even if they are not measurably amphiphilic. However, when these ‘sort-of lipids’ are inserted into lipid systems whose physical behaviour is well understood, their influence on the character of the system is measurable.  This influence of the added component is also described as concentration-dependent, i.e., the more of the molecule that is put in (the higher the concentration), the stronger the given effect.
Some of the most amazing and unexpected behaviour of lipids occurs when they are exposed to water.  As part of the molecule likes water, and part of it does not, you can imagine that this situation is not going to be simple for the poor little lipid.  We as scientists describe the stresses and strains in systems like these according to the laws of thermodynamics.  Those of a certain generation may like to remind themselves of the Flanders and Swann song at this point.  Either way, we have put an unsuspecting lipid into a system with water and so what does it do?  Generally, lipids will self-assemble.  The exact manner in which this occurs varies between types of lipid, but the principle is observable across all of them.

The principle of self-assembly can be explained in terms of two competing priorities.  Thermodynamics means that the grease-loving (lipophilic) part of the lipid molecule wants to be shielded from the water, but at the same time, the water-loving (hydrophilic) part wants to be in touch with the water.  As our lipid cannot bear to disobey the laws of thermodynamics (who would?), it arranges itself in order to compromise between these competing forces.  This compromise can also be described in terms of energy.  In order to adopt a position in which the greasy section is exposed to water requires a lot of energy.  When the energy that is available to the system is insufficient for this, exposing the greasy section of the lipid to the water is described as energetically unfavourable.  This is the thermodynamic law I refer to and is also known as the hydrophobic effect.  The latter term, as you might well guess, is from the Greek ‘hydro-‘ meaning ‘water’ and ‘‑phobic’ meaning ‘hating’.

The hydrophobic effect may sound obscure, but the forces involved in it are what hold the membranes of cells together.  This means it has a huge and unsung part to play in understanding biology.