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Posts Tagged ‘cholesterol

how statins work 4: blocking the mevalonate pathway and the question of side-effects

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I may be going into this topic in too much detail, but I’m enjoying what I’m learning along the way, and our biochemistry is enormously complex and fascinating and worth knowing a lot about for its own sake as well as a guard against false claims and over-simplification. I haven’t yet ordered Ben Goldacre’s new book Do statins work?: the battle for perfect evidence-based medicine, which might render all this (superficial) research superfluous, but I doubt it…. [I’ve since discovered that the book won’t be available for quite a while – I wonder what’s holding it back, as clearly it has already been written…]

So I left off with the production of citrate. Thiol (HS) groups, like alcohol (HO) groups can be linked to carboxylic acid groups. The alcohol group can be taken from the carboxylic acid group and the hydrogen from the thiol group, and these can be combined to create water molecules. The sulphur atom is bound to the carbon of the carboxylic acid group, and this is called a thioester link (similar to an ester link but with a thiol rather than an alcohol group). The resulting molecule is Acetyl-CoA. Acetyl is essentially acetic acid with the alcohol group removed.

Oxaloacetate combines with Acetyl-CoA and water to create citrate. The water molecule is involved in breaking the thioester link, via hydrolysis, between the carbon atom (of the carboxylic acid group of the acetic acid molecule), and the sulphur atom of the coenzyme A. These are connected by a covalent bond, in which two electrons are shared, one from the carbon and one from the sulphur. This hydrolytic process results in an alcohol group combining with the carbon atom, with the other hydrogen atom combining with the sulphur to recreate a coenzyme A (CoA-SH).

A break in the covalent bond between oxygen and carbon in the ketone group of the oxaloacetate molecule, as well as a break in the covalent bond in the methyl group of the acetic acid component of the Acetyl-CoA molecule, leads to a new molecule with an extra deprotonated carboxylic acid group, the conjugate base of citric acid, i.e. citrate. The conversion is catalyzed by the enzyme citrate synthase.

Next is the transportation of citrate into the inter-membrane space of the mitochondrion. A protein (SLC25A1) magically transports the citrate into the inter-membrane space from where it diffuses through the outer membrane into the cell cytoplasm. The citrate then undergoes a reverse process, thanks to an enzyme called ATP citrate lyase, I won’t go into all the details here, but oxaloacetate is recreated, a condensation reaction occurs, and ADP and inorganic phosphate is formed. The oxaloacetate is returned to the mitochondrial matrix in the form of pyruvate, via malate. We now have Acetyl-CoA in the cytoplasm, and the pyruvate is transported by another protein (SLC16A1) back into the matrix, completing the cycle, as the pyruvate is reconverted to oxaloacetate. As I’ve pointed out, there’s a lot more to this cycle, in terms of enzymes, hydrolysis, ATP and ADP, but we’re now at the point where we can look at cholesterol synthesis in the cytoplasm.

The first stage of this is the formation of mevalonate. Three Acetyl-CoA molecules are required for this. So, according to the videos I’m relying on, the first reaction joins together two Acetyl-CoA’s. This involves breaking a bond between the carbon and the sulphur atom in one (which sends one electron back to the carbon, the other back to the sulphur), and in the other, breaking a bond between carbon and hydrogen. Then the free-electron carbon is bound to the other molecule’s free-electron carbon. This results in a molecule with a methyl group (CH3), a carbonyl group (C=O), a methylene group (CH2<) and a carboxyl group (COOH) bound to the coenzyme A molecule by a thioester link. In the same reaction the hydrogen atom is bound to the sulphur atom to recreate an intact molecule of coenzyme A, with its thiol group. All of this is a reversible reaction catalysed by an enzyme in the cytoplasm called Acetyl-CoA Acetyl Transferase, and the resulting molecular product is called Acetoacetyl-CoA. This is the result of binding two Acetyl-CoA’s together, and the next step is to bind a third Acetyl-CoA to this molecule. This involves breaking one of the carbon-oxygen bonds in the Acetoacetyl-CoA molecule, breaking a carbon-hydrogen bond in the new third molecule, and introducing a water molecule to hydrolyse the thioester link. The free-electron carbons from the two molecules are bound together, and the hydrogen from the new molecule is bound to the oxygen. The product is catalysed by the enzyme HMG-CoA synthase, and the name of the product is HMG-CoA, aka beta-hydroxy-beta-methylglutaryl-CoA. The ‘beta’ refers to the middle carbon in the 5-carbon chain, to which the methyl and alcohol groups are attached.

So, we’re now at the stage of having produced HMG-CoA. The next reaction is vitally important for a couple of reasons. It’s the rate-limiting step for the entire biosynthesis of cholesterol, and it’s the site of action of statins, which block the synthesis here by blocking the enzyme that catalyses this reaction. That enzyme is called HMG-CoA reductase, and the various statins that can block this enzyme have names such as simvastatin, atorvastatin and rosuvastatin.

So I’ll try to make sense of this step, then I’ll go back to how statins interfere with it. HMG-CoA reductase catalyses the reaction which transforms HMG-CoA into mevalonate. This reaction requires two molecules of reduced NADP (2NADPH) which carry hydride anions, and also two protons (2H+). This effectively brings in four neutral hydrogen atoms, resulting in the creation of two oxidised NADP molecules (2NADP+). A thioester link in the HMG-CoA is broken, ultimately recreating a coenzyme A with an intact thiol group and and an aldehyde group. Also one of the bonds between the carbon and the oxygen can be broken, allowing for the binding of other hydrogens, in such a way that two hydrogen atoms are bound to the end carbon of the molecule, as well as an alcohol group. This is the mevanolate molecule, to which phosphate groups are added, converting it to ‘activated isoprenes’.

So the question of whether inhibiting of HMG-CoA reductase by statins has effects beyond the inhibition of cholesterol production de novo, is obviously essential, so I won’t be focusing so much on cholesterol biosynthesis from here, I’ll be looking, in my amateur way, at claims that the inhibition of HMG-CoA reductase by statins can sometimes have somatic side-effects, including SAMS (statin-associated muscle symptoms) ‘which are the most well-documented side effect of statins, although there appears to be no unifying mechanism’, according to this research article published in Circulation Research. Note the vagueness of this acronym, which might be seen as a red flag. Circulation Research is a journal of the American Heart Association, and looks pretty kosher to me, so I will rely on it heavily in this and possibly other posts. The article is also pretty up-to-date having been published earlier this year (2019).

The article summarises the mechanism of action of statins in a single paragraph which I’ll reproduce here, because it also reports on possible positive pleiotropic effects:

Statins work by competitively blocking the active site of the first and key rate-limiting enzyme in the mevalonate pathway, HMG-CoA reductase. Inhibition of this site prevents substrate access, thereby blocking the conversion of HMG-CoA to mevalonic acid. Within the liver, this reduces hepatic cholesterol synthesis, leading to increased production of microsomal HMG-CoA reductase and increased cell surface LDL receptor expression. This facilitates increased clearance of LDL-c from the bloodstream and a subsequent reduction in circulating LDL-c levels by 20% to 55%. In addition to reducing LDL-c and cardiovascular morbidity and mortality, statins may have additional non–lipid-related pleiotropic effects. These include improvements in endothelial function, stabilization of atherosclerotic plaques, anti-inflammatory, immunomodulatory and antithrombotic effects, effects on bone metabolism, and reduced risk of dementia. These additional benefits are primarily thought to arise because of inhibition of the synthesis of isoprenoid intermediates of the mevalonate pathway.

Pleiotropy is a term I’m just learning about. A pleiotropic gene is one that ‘exhibits multiple phenotypic expression’. For our purposes, the word ‘multiple’ is key. The point here is that the blocking of HMG-CoA reductase may have multiple benefits, not all related to high LDL-c levels, which raises the obvious question about the positive purposes of HMG-CoA reductase production. As to the harms or side-effects, the article has this to say:

Currently, no universally accepted definition of statin toxicity/intolerance exists, with several groups attempting to define the condition. The prevalence of statin intolerance is also widely debated, in part because of difficulties in identification and diagnosis, particularly with respect to muscle symptoms. Observational studies suggest it occurs in 10% to 15% of patients, with clinic data putting it as high as 30%. In randomized controlled trials, the incidence is thought to be 1.5% to 5% of patients, although this is believed to be an underestimation as most studies exclude patients with a history of statin intolerance either before randomization or during the run-in period.

As can be seen, it’s very difficult to find a reliable rate of statin intolerance or toxicity, or even a reliable definition of same – the article lists four separate definitions from different associations monitoring lipid problems and atherosclerosis. It concludes the section with this statement:

Despite the difficulties in identifying and diagnosing statin toxicity, however, several international organizations have identified statin intolerance to be of major clinical importance that warrants further research and investigation.

Clearly the statin wars – if I can be so controversial as to use such a term – are far from over. I’ll continue to educate myself about the issue and promise to write more in the future.

it’s complicated


Cholesterol biosynthesis part 3, by Ben1994 (video)

Cholesterol biosynthesis part 4, by Ben1994 (video)

Written by stewart henderson

October 19, 2019 at 6:50 pm

how statins work 3: the beginnings of cholesterol, from Acetyl-CoA

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Coenzyme A – an acetyl group attaches to the -SH shown in red

So how is cholesterol made in the body? We need to know this in order to understand how statins inhibit or interfere with this process.

I’ve shown the actual structure of cholesterol in part 1 of this series, but remember it’s a sterol, which is a steroid – four carbon rings with hydrogen atoms attached – in which one of the hydrogens is replaced by an alcohol group. The particular form of sterol called cholesterol, with a 7-carbon chain attached to the end-carbon ring (the D ring), and three methyl groups attached to specific carbons in the rings and chain (it’s better to look at the skeletal structure in part 1). There are precisely 27 carbon atoms specifically placed within the molecule.

I’m using a set of videos to understand how cholesterol is synthesised – it might be best to look at them yourself, but I’m writing it all down to improve my own understanding. So we start by understanding something about acids and their conjugate bases. Apparently an acid is a molecule which is capable of donating protons into solution. Take pyruvic acid and its conjugate base pyruvate. Here’s what Wikipedia says about them:

Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO, is a key intermediate in several metabolic pathways throughout the cell.

I don’t understand the first sentence, but no matter, pyruvic acid is a 3-carbon molecule with a carboxylic acid at one end and a ketone group in the middle of the molecule (according to Britannica, a ketone is ‘any of a class of organic compounds characterized by the presence of a carbonyl group in which the carbon atom is covalently bonded to an oxygen atom. The remaining two bonds are to other carbon atoms or hydrocarbon radicals)’. The proton that comes off the oxygen of the alcohol group of the pyruvic acid can be donated into the surrounding solution, increasing its acidity. The pyruvic acid is thus transformed into its negatively charged conjugate base (it’s no longer capable of donating protons but it can receive them). This is the case with all acids in the cytoplasm of cells. As inferred in the quote above, conjugate bases are vital components of biosynthetic pathways. Most of the molecules in the cytoplasm will exist as pyruvate at a physiological pH of around 7.5.

Next – and hopefully this will become clear eventually – we’re going to look at two molecules, NAD+ (nicotinamide adenine dinucleotide) and NADP+ (nicotinamide adenine dinucleotide phosphate). They transport electrons, and are capable of accepting a hydride anion, which is a hydrogen atom with a negative charge. The normal hydrogen atom, called protium, has a proton and an electron only. When it donates away its electron it becomes a hydrogen cation, and when it gains an electron it becomes a hydride anion.

NAD+ is an adenine organic base bound to a ribose sugar. Then there are two phosphate groups coming off the ribose sugar, the second of which attaches to another ribose sugar. This second ribose sugar has nicotinamide attached to it (see below),

in which the phosphate groups are magenta-coloured circles. To explain something about ribose sugars, here’s something from Pearson Education:

The 5-carbon sugars ribose and deoxyribose are important components of nucleotides, and are found in RNA and DNA, respectively. The sugars found in nucleic acids are pentose sugars; a pentose sugar has five carbon atoms. A combination of a base and a sugar is called a nucleoside. Ribose, found in RNA, is a “normal” sugar, with one oxygen atom attached to each carbon atom. Deoxyribose, found in DNA, is a modified sugar, lacking one oxygen atom (hence the name “deoxy”). This difference of one oxygen atom is important for the enzymes that recognize DNA and RNA, because it allows these two molecules to be easily distinguished inside organisms.

So, just for my own understanding, nucleotides include phosphate groups. NAD+ is a dinucleotide, with two nucleotides (ribose sugars with phosphate groups attached), attached to adenine and to nicotinamide molecules. Also, NAD+ has a positive charge around the nicotinamide – on its nitrogen atom.

NAD+ becomes neutralised by accepting a hydride anion (one proton and two electrons) and becomes NADH, or reduced NAD. Now, remembering NADP+, it has an extra phosphate group on the ribose sugar of the adenine nucleotide (also called an organic base, apparently). Like NAD+, NADP+ can accept a hydride anion (becoming reduced NADP) and then later exchange it in another reaction. Effectively these molecules are electron carriers, collecting electrons and transporting them to where they’re needed for other reactions.

Now to introduce something else completely new for me – Acetyl-CoA (acetyl coenzyme A). A quick grab again, this time from Wikipedia:

Acetyl-CoA is a molecule that participates in many biochemical reactions in protein, carbohydrate and lipid metabolism. Its main function is to deliver the acetyl group to the citric acid [Krebs] cycle to be oxidized for energy production

Acetyl-CoA is found, and presumably produced, in mitochondria, and as part of this cholesterol-synthesising pathway it needs to be removed from the ‘mitochondrial matrix’. What’s that, I ask. So here’s a bit about the mitochondrial matrix, from yet another source, this time

The mitochondrion consists of an outer membrane, an inner membrane, and a gel-like material called the matrix. This matrix is more viscous than the cell’s cytoplasm as it contains less water. The mitochondrial matrix has several functions.It is where the citric acid cycle takes place. This is an important step in cellular respiration, which produces energy molecules called ATP. It contains the mitochondrial DNA in a structure called a nucleoid. A mitochondrion contains its own DNA and reproduces on its own schedule, apart from the host cell’s cell cycle. It contains ribosomes that produce proteins used by the mitochondrion. It contains granules of ions that appear to be involved in the ionic balance of the mitochondrion.

So basically this matrix is like (or equivalent to) the cell’s cytoplasm, only more viscous, and contains ribosomes, one or more nucleoids and ionic granules, inter alia.

Acetyl-CoA is essential to the biosynthesis of cholesterol, and is found initially in the mitochondrial matrix, and we need to look at the pathway for its removal from that matrix into the cytoplasm, where all the action occurs.

Intruding into the mitochondrial matrix from the (quite impermeable) inner cell membrane are the cristae, which give the membrane more of a surface layer for interactions. This inner membrane is the site of oxidative phosphorylation. What’s that, I ask. Well, it’s key to the production of ATP, and at least I know that ATP is the ‘energy molecule’, and that it’s produced in mitochondria. Here’s something about the process from Khan Academy:

Oxidative phosphorylation is made up of two closely connected components: the electron transport chain and chemiosmosis. In the electron transport chain, electrons are passed from one molecule to another, and energy released in these electron transfers is used to form an electrochemical gradient. In chemiosmosis, the energy stored in the gradient is used to make ATP.

So a strong proton gradient is built up across the inner membrane of the mitochondrion. It’s a concentration gradient but also an ‘electrical potential difference’ gradient, so that the electrical potential within the matrix is lower, by some 160 millivolts, than that across the inter-membrane space. The protons within this space are unable to pass back into the matrix. The only way they can get back into the matrix is by means of ATP synthase which can harness the energy from the protons as they move down the chemical and electrical gradient, and use that energy to bind ADP to inorganic phosphate to create ATP.

I don’t fully understand all that, but the main point here is that the mitochondrial inner membrane is very ‘tight’, which makes it difficult to transfer Acetyl-CoA out of the matrix and into the inter-membrane space, from which it can more easily diffuse through the more permeable outer membrane into the cytoplasm.

The structure of Acetyl-CoA: it consists of an acetic acid molecule (CH3COOH) with a thioester link to the thiol group of a coenzyme A molecule. The importance for us here is this thiol (HS) group, which is similar structurally to an alcohol (HO) group, as sulphur has similar properties to its periodic table neighbour, oxygen. So thiol groups can be linked to carboxylic acid groups as alcohol groups can. Acetyl essentially means acetic acid with the alcohol removed. To get this Acetyl-CoA out of the matrix, it is first bound to oxaloacetate, a four-carbon molecule, to create citrate, the first molecule of the citric acid cycle. This citrate can be passed through the mitochondrial inner membrane and into the cytoplasm where it can be converted back into Acetyl-CoA.

So the conjugate base, oxaloacetate, has carboxylic acid groups, attached to the first and fourth carbon atoms, that have lost their protons into solution. An enzyme within the matrix is able to combine oxaloacetate with Acetyl-CoA and water to create citrate…

Okay, this is proving to be a much longer story than I might’ve hoped, but I like to be thorough – and in reality I’m still not being thorough enough. There’s a lot of rubbish on the internet about statins, much of it self-serving in one way or another, so I’ll just keep plodding along until I feel at least halfway informed about the matter. Meanwhile, you just keep getting on with your work, and don’t mind me.


Cholesterol biosynthesis part 1, by Ben1994, 2015

Cholesterol biosynthesis part 2, by Ben 1994, 2015

Written by stewart henderson

October 14, 2019 at 5:26 pm

How statins work 2: atherosclerosis and LDL cholesterol

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Recent studies have revealed that children 8-10 years old are being diagnosed with Type II diabetes, high cholesterol, and high blood pressure at an alarming rate.

Lee Haney

Picture taken from ‘LDL in atherosclerosis and heart disease’ by Axel Sigurdsson, MD, PHD

As I said in my previous post, biochemistry is almost infinitely complex, so bear with me as I crawl towards an understanding of the role of statins in reducing LDL cholesterol in the blood stream, thus reducing atherosclerosis, a major feature of heart disease.

Remembering, first, that cholesterol is a sterol, which is a modified steroid with a hydroxyl (alcohol) group coming off carbon 3. It’s a mostly hydrophobic lipid with this tiny polar hydroxyl group added. It’s carried around in the bloodstream by lipoproteins.

I’ll turn now to atherosclerosis – though I don’t currently know whether statins can perform roles other than reducing the build-up of plaque in the arteries.

So, generally, our arteries carry oxygenated blood from the heart to other organs and regions of the body. Atherosclerosis is sometimes called ‘hardening of the arteries’, as sklerosis is from Greek, meaning ‘hardening’, but it’s really a narrowing rather than a hardening, or perhaps it’s better described as both, as we’ll see. Arteriosclerosis is a more general name, while atherosclerosis means blockage or narrowing (stenosis) due to an atheroma, an abnormal accumulation of ‘debris’ or plaque consisting of fat (mostly), calcium and sometimes fibrous tissue in the inner arterial wall (endothelium). These atheroma are difficult to detect before they cause heart attacks or disease, because heart arteries are very small and hidden deep within the chest. They’re also quite mobile and elastic with blood flow. Heart attack and stroke sometimes happen when the atheroma ‘bursts’ – the fibrous cap (of smooth muscles cells, cholesterol-rich foam cells, collagen and elastin) which surrounds the atheroma is ruptured, or breaks free from the arterial wall, causing a blood clot (thrombus). These are sudden events, not easily detected beforehand. Alternatively, major problems arise when the atheroma becomes large enough to defeat arterial flexibility.

There can be symptoms, apart from such major dramas as heart attacks and stroke, which may act as warning signs for atherosclerosis. The narrowing of the arteries means that less blood and oxygen is reaching the cardiovascular system (ischemia), and this may result in vomiting, angina (chest pain), and general feelings of faintness and anxiety. Atherosclerosis of the carotid artery, which feeds the brain, may have different symptoms, including headaches, dyspnea and facial numbness. Atherosclerosis can also affect the function of the liver, kidneys and other organs, and the vascular system.

So what causes atheromas? It seems that these accumulations of plaque are the result of monocyte-macrophage activity. Macrophages are types of white blood cells (leucocytes) that perform immune and cleansing functions. However, we don’t really know why the plaque build-up occurs – though it might be initiated by damage to the endothelium. We do know that atherosclerosis can begin early, and that blood LDL cholesterol is a major factor in the activity that leads to this build-up. That’s why researchers have been rather single-minded about ways of reducing LDL cholesterol, and even on increasing HDL cholesterol levels, though there’s little evidence, apparently, that higher HDL levels are beneficial. Nor, interestingly, is there much evidence that lowering triglycerides has a positive effect on heart disease, while study after study has shown that low LDL cholesterol levels are key to avoiding cardiovascular problems.

Okay, now I’m going to take a few steps back to look more deeply at the role of LDL cholesterol in building atheromas and so causing atherosclerosis. Returning to my vague mention of macrophages and monocytes, here’s a clearer picture, drawn mainly from this excellent video.

  1. Structure of arterial wall

First, we need to know that the arterial walls are layered. The first layer surrounding the lumen (the tunnel space where the blood flows and where you find red blood cells or RBCs, leukocytes and lipoproteins, etc) is the epithelium, a thin layer of squamous cells. This layer is surrounded by the tunica intima (sometimes the epithelium is described as part of the T intima), an elastic layer quite rich in collagen. It also contains structural cells called fibroblasts, and smooth muscle cells (SMCs). Surrounding the T intima is the tunica media (particularly rich in SMCs), which in turn is surrounded by the thicker, tougher tunica adventitia. In general, the arterial wall becomes stiffer and more fibrous as you move from inner to outer. Atherosclerosis is apparently more of a problem in large and middle-sized arteries which contain more of the protein elastin.

2. Plaque formation

Plaque formation begins, it’s believed, when there’s damage to the thin endothelial layer (only one cell thick) as well as an abundance of circulating low density lipoproteins (LDLs). LDLs (mostly lipid with a small amount of protein) can then move through the damaged layer into the T intima where they become oxidised by ‘reactive oxygen species’ (free radicals) and other enzymes such as metallo-proteases, released by the endothelial cells. These oxidised LDLs, which are now ‘trapped’ in the T intima, will activate endothelial cells to express receptors for white blood cells (leukocytes), particularly the largest types of leucocyte, known as monocytes. So we have this accumulation of oxidised LDLs activating endothelial cells to express adhesion molecules for leucocytes, which brings monocytes and T helper cells into the T intima layer. This movement into tissue transforms monocytes into macrophages (not sure how that happens), and these macrophages then ‘take up’ or engulf the oxidised LDLs and form foam cells. By this time the lipid material dumped into the T intima has created something like a lake of fat, known as a ‘fatty streak’. Foam cells are central to the process of plaque formation and atherosclerosis, as they induce more SMCs into the T intima from the T media by means of a released growth factor, IGF-1 (insulin-like growth factor), and this leads to increased synthesis of collagen in the region, which hardens the plaque build-up, a build-up further fostered by foam cell death which releases more lipid material. Foam cells also release pro-inflammatory cytokines and reactive oxygen species as well as chemokines which attract more macrophages to the site. Upon death they also release DNA material that attracts neutrophils, a very common type of white blood cell. All of this will increase inflammation or plaque build-up in the region.

3. Effects

As mentioned, SMCs contribute to the containment of this inflamed lipid area by releasing proteins such as collagen and elastin, which is used to build a fibrous cap around it. They also stiffen the formation, the atheroma as it’s called, by adding calcium. All of this has the effect of enlarging the atheroma and so reducing the diameter of the arterial lumen in the area, which raises blood pressure as the blood tries to maintain an adequate flow. The calcification of the area also considerably reduces the flexibility of the arterial wall, again resulting in increased blood pressure. Rupture of the fibrous cap may result, which may lead to thrombosis.

So where do statins come in here? Let me quote from an abstract of one academic paper: Statins in atherosclerosis: lipid-lowering agents with antioxidant capabilities, published in 2004:

Statins (3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors) are the first-line choice for lowering total and LDL cholesterol levels and they have been proven to reduce the risk of CHD [chronic heart disease]. Recent data suggest that these compounds, in addition to their lipid-lowering ability, can also reduce the production of reactive oxygen species and increase the resistance of LDL to oxidation. It may be that the ability of statins to limit the oxidation of LDL contributes to their effectiveness at preventing atherosclerotic disease.

Note that oxidation of LDL has the effect of fixing it in the T intima, as mentioned above, so if it’s true, as I presume it is, that statins inhibit LDL oxidation, as well as having other benefits, then they can’t be a bad thing, as long as there aren’t serious side-effects. I’ll continue to explore this topic, as it’s teaching me a lot about the blood, the liver and the circulatory system, inter alia – and it’s great fun. Dr Ben Goldacre has written a book Do statins work? the battle for perfect evidence-based medicine, which hasn’t been released yet, but I intend to get my hands on it and devour it, along with more videos and articles. In the meantime I hope it’s not too controversial to go on saying that the best way to reduce that nasty (but not too nasty) LDL cholesterol is to eat a healthy diet and engage in effective exercise.

PS: haha I know this’ll be unreadable to most, but if anybody finds any egregious error in this, let me know.


Atherosclerosis video – Nucleus Medical Media (2009)

Atherosclerosis – pathophysiology, video by Armando Hasudungen (2014)

Atherosclerosis – part 1, Khan Academy video

Cholesterol metabolism part 1, video by Ben1994 (2015)

Cholesterol metabolism part 2, video by Ben1994 (2015)

Cholesterol metabolism part 3, video by Ben1994 (2015)

Written by stewart henderson

September 21, 2019 at 5:20 pm

How statins work 1 – stuff about cholesterol, saturated fats and lipoproteins…

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filched from Wikipedia – don’y worry, I don’t understand it either – at least not yet

Statins are HMG-CoA reductase inhibitors, according to Wikipedia’s first sentence on the topic. HMG-CoA reductase is an enzyme – a macromolecule that accelerates or catalyses chemical reactions in cells. The enzyme works in the mevalonate pathway, which produces cholesterol and other terpenoids (terpenoids are very common, varied and useful forms of hydrocarbon).

So what does HMG-CoA stand for, and what’s a reductase?

3 hydroxy -3 methyl-glutaryl coenzyme A, which may be explained later. A reductase is an enzyme which catalyses a reduction reaction, and I’m not sure if that refers to redox reactions, in which case reduction involves the gaining of electrons…

But let’s look at cholesterol, which statins are used against. Sterols are lipid molecules with a polar OH component, and ‘chole’, meaning bile, comes from the liver. So cholesterol is a type of lipid molecule produced largely by the liver or hepatic cells of vertebrate animals. Cholesterol is essential for life, and it’s synthesised in the cell via a complex 37-step process (the mevalonate pathway makes up the first 18 of these). It makes up about 30% of our cell membranes, and its continual production is necessary to maintain cell membrane structure and fluidity. In high food-intake countries such as Australia and the US, we ingest about 300mg of cholesterol a day on average. We also have an intake of phytosterols, produced by plants, which might vary from 200-300mgs. Of course, this is massively dependent on individual diets (increased phytosterol intake may reduce LDL cholesterol, but it comes with its own quite serious problems).

The (very basic) structure of cholesterol is shown below.

The body of the molecule (centre) contains 4 rings of carbon and hydrogen – A, B and C are 6-carbon rings, while D has 5. The bonds between rings A and B, and C and D, represent methyl groups. On the left is a hydroxyl group, which is hydrophilic and polar, though the massive body of the molecule is extremely hydrophobic, which is reinforced by the cholesterol tail connected to the D ring. The hydroxyl polarity creates a binding site, which builds structure as the molecule binds to others.

Interestingly, the need for cholesterol synthesis varies with temperature, or climate. This has to do with fluidity and melting points. People who live in colder climates require less cholesterol production because, in cold weather, solid structure remains intact. Hotter climates cause greater fluidity and increased entropy, so more cholesterol needs to be synthesised to create and maintain structure.

So now to the 18-step mevalonate pathway, by which the liver produces lanosterol, the precursor to cholesterol. Well, on second thoughts, maybe not… It’s fiendishly complex and Nobel Prizes have been deservedly won for working it all out and I’m currently thinking that physics is easy-peasy compared to biochemistry (or maybe not). What I’m coming up against is the interconnectivity of everything and the need to be thorough. For example, in order to understand statins we need to understand cholesterol, and in order to understand cholesterol we need to understand lipids, lipoproteins, the liver, the bloodstream, the digestive system… So I sometimes feel overwhelmed but also annoyed at the misinformation everywhere, with chiropractors or ‘MDs’ announcing the ‘truth’ about statins, cholesterol or whatever in 500-word screeds or 5-minute videos.

Anyway, back to work. Cholesterol is a lipid molecule, and lipids are generally hydrophobic (they don’t mix with water, or to be more exact they’re not very soluble in water), but cholesterol has a hydrophilic hydroxyl side to it. Lipids that have this hydrophilic/hydrophobic mix are called amphipathic. Phospholipids in cell membranes are an example. and they interact with cholesterol in the ‘phospholipid bilayer’. As an indication of the complexity involved, here’s a quote from an abstract of a biochemical paper on this very topic:

Mammalian cell membranes are composed of a complex array of glycerophospholipids and sphingolipids that vary in head-group and acyl-chain composition. In a given cell type, membrane phospholipids may amount to more than a thousand molecular species. The complexity of phospholipid and sphingolipid structures is most likely a consequence of their diverse roles in membrane dynamics, protein regulation, signal transduction and secretion. This review is mainly focused on two of the major classes of membrane phospholipids in eukaryotic organisms, sphingomyelins and phosphatidylcholines. These phospholipid classes constitute more than 50% of membrane phospholipids. Cholesterol is most likely to associate with these lipids in the membranes of the cells.

Anyway, perhaps for now at least I won’t explore the essential role of cholesterol in cell structure and function, but the role of ingested cholesterol, the difference between LDL and HDL cholesterol, and how it relates to saturated fats and heart disease, particularly atherosclerosis. As Gregory Roberts explains it in a Cosmos article, saturated fats (found in butter, meat and palm oil) definitely raise total cholesterol…

But what is saturated fat, as opposed to polyunsaturated or mono-unsaturated fat? Most of us have heard of these terms but do we really know what they mean? Here comes Wikipedia to the rescue (because there’s a lot of bullshit out there):.

saturated fat is a type of fat in which the fatty acid chains have all or predominantly single bonds. A fat is made of two kinds of smaller molecules: glycerol and fatty acids. Fats are made of long chains of carbon (C) atoms. Some carbon atoms are linked by single bonds (-C-C-) and others are linked by double bonds (-C=C-). Double bonds can react with hydrogen to form single bonds. They are called saturated, because the second bond is broken and each half of the bond is attached to (saturated with) a hydrogen atom. Most animal fats are saturated. The fats of plants and fish are generally unsaturated. Saturated fats tend to have higher melting points than their corresponding unsaturated fats, leading to the popular understanding that saturated fats tend to be solids at room temperatures, while unsaturated fats tend to be liquid at room temperature with varying degrees of viscosity (meaning both saturated and unsaturated fats are found to be liquid at body temperature).
Various fats contain different proportions of saturated and unsaturated fat. Examples of foods containing a high proportion of saturated fat include animal fat products such as cream, cheese, butter, other whole milk dairy products and fatty meats which also contain dietary cholesterol. Certain vegetable products have high saturated fat content, such as coconut oil and palm kernel oil. Many prepared foods are high in saturated fat content, such as pizza, dairy desserts, and sausage.
Guidelines released by many medical organizations, including the World Health Organization, have advocated for reduction in the intake of saturated fat to promote health and reduce the risk from cardiovascular diseases. Many review articles also recommend a diet low in saturated fat and argue it will lower risks of cardiovascular diseases, diabetes, or death. A small number of contemporary reviews have challenged these conclusions, though predominant medical opinion is that saturated fat and cardiovascular disease are closely related.

Saturated Fat, Wikipedia. I’ve removed links and notes – they’re just too much of a good thing! Apologies for the lengthy quote but I think this is essential reading in this context.

High density lipoprotein (HDL) cholesterol can be a problem if your levels are low. HDL absorbs cholesterol and carries it back to the liver, from where it’s removed from the body. So generally high levels of HDL will reduce your chances of heart attack and stroke.

As Roberts notes, from the 1950s, heart disease has risen to be a major problem. Heart attack victims have been regularly found to have arteries clogged with ‘waxy plaques filled with cholesterol’. Further proof that cholesterol was to blame came with studies of people with a genetic disease – familial hypercholesterolemia (FH) – which meant that they had some five times the normal levels of blood cholesterol, and suffered heart attacks even as children or teenagers. Also, the rise in blood cholesterol levels and the rise in heart attacks, and heart disease generally, were correlated. This was unlikely to be coincidental.

But what’s a lipoprotein and why the different densities? Here we get into another area of extraordinary complexity. Lipoproteins are vehicles for transporting hydrophobic lipid molecules such as cholesterol, triglycerides and phospholipids through the watery bloodstream or the watery extracellular fluid (blood plasma – the yellowish liquid through which haemoglobin and lipoproteins etc are transported – is a proportion of that fluid). They act as emulsifiers, ‘encapsulating’ the lipids so that they can mix with and move through the fluid. Lipoproteins don’t just come in HD and LD forms – we classify them in terms of their density much as we classify colours in the light (electromagnetic) spectrum. According to that density classification we recognise five major types of lipoprotein in the bloodstream.

Cholesterol arrives in the blood via endogenous (internal) and exogenous (external) pathways. Some 70% of our cholesterol is produced by the liver, so, though diet is an important facet of changing cholesterol levels, finding ways of modifying or blocking liver production was clearly another option. Through studying the way fungi produced chemicals such as penicillin that break down cell walls (a large part of which are cholesterol), Akira Endo was the first to produce a statin from a mould in oranges – mevastatin. That was the beginning of the statin story.


Cholesterol metabolism, part one – video by Ben1994 (excellent)

Cholesterol structure, part 1/2, by Catalyst University

Written by stewart henderson

September 15, 2019 at 10:24 am

want to live to 100?

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… It may destroy diseases of the imagination, owing to too deep a sensibility, and it may attach the affections to objects, permanent, important, and intimately related to the interests of the human species.

Humphry Davy,  on the value of science, in ‘Discourse introductory to a  course of lectures on chemistry’, 1802


A great many of us would like to live a long and healthy life, with a greater emphasis on health than length. But both please, if possible, thanks.

I’ve been reading the issues of New Scientist: the collection as they come out. The first issue dealt with the Big Questions, namely Reality, Existence, God, Consciousness, Life, Time, Self, Sleep and Death. Bit of a roller coaster ride, leaving me dizzy, confused, but often enlightened, and sometimes even exhilarated. So, better than a roller coaster. The second issue, entitled The Unknown Universe, took me far out beyond multiverses, quantum loops, energetic dark matter and the eventful horizons of black holes, and essentially taught me that modern cosmology is a mess of competing theories, often competing, it seemed, to be the most egregious ideas that are compatible with mathematical possibility. However, it may be that the studious avoidance of scary maths in these essays/summaries may have made them seem more loopy (or strangulatingly stringy) than they are.

The third issue was more down to earth, and not only earth but me, and you, dear reader. It’s entitled The scientific guide to a better you, and it’s all about longevity, health and success.

So what’s the secret, at least for the first two? Basically, eat healthily, with not too much meat, make sure you have good genes, don’t be too much of a loner (too late for me, I’ve been a loner for 40 years, and that’s unlikely to change, but I’l try, as I always say), be intelligent, active and exploratory. That’s the message of the first half of this issue anyway.

What interested me, though, was the detail. Measurements. Blood sugar, cholesterol, heart rate and many other factors and parameters, most of which I didn’t know I had to be concerned about. The various essays are peppered with these measures of health or lack thereof, but how does your average Jo like me get a measure of these things without pestering doctors on a weekly basis about wellness instead of sickness?

So, for fun, I thought I’d look into these ways of measuring ourselves and see if we can manage them from home. A sort of practical guide to centenarianism and beyond.

1. Body mass index (BMI)

Your BMI is a very rough-and-ready guide to whether or not you’re a healthy weight for your height. Various websites can calculate this for you instantly if you know your height and weight. My current BMI is 26, according to the Heart Foundation, which it regards as ‘overweight’, though very close to the borderline between ‘overweight’ and ‘healthy’. About three years ago my BMI was 29, well into the overweight category, in fact getting close to obese. I decided to eat less, without fasting or ‘going on a diet’, and to try to up my exercise, and over a 2-year period I brought my BMI down from 29 to 23, well into the healthy range. Since then it has crept back up to 26, and I’m struggling to get it back down again. I just need to lose a couple of kilos, and keep them off. The myriad other ways of measuring your health these days might make the old BMI seem outmoded – it doesn’t measure your fat to muscle ratio, for example, or the amount of fat around your heart and other organs – but I find it a useful guide for me, and the cheapest available.

2. Heart rate/blood pressure

Measured in beats per minute, your heart rate naturally varies with exertion, and also with anxiety, stress, illness, drug use and so on. The normal resting heart rate for an adult human ranges from 60 to 100 bpm. You can measure your own heart rate (your pulse) at any time by finding an artery close to the surface. The radial artery on the wrist, the one you see heading in the direction of the thumb, is commonly used due to ease of location, but don’t try it with your thumb which has its own strong pulse. I’ve just located my own wrist pulse and measured it as 62bpm. That’s the first time I’ve ever done it. However, I imagine it would be harder to measure after a bout of HIIT (high intensity interval training), which I sometimes indulge in, or after a moderately strenuous bike-ride. It would be even harder while you’re in the middle of exercise, so that’s where heart rate monitors, including those that can be worn on the wrist, come in handy. A quick google-glance tells me that such wrist devices are selling at $100 to $150. However, caveat emptor, as doubt is being cast on their accuracy. Electrocardiographs (ECGs, or EKGs), which measure the electrical activity of your heart, provide a much more accurate record than heart rate monitors, which are apparently only really effective when you’re at rest. One of the problems is that these optical monitors use light to track your blood, and to get an ‘accurate’ reading, you need to be very still, which sort of defeats the purpose. Reporter Sharon Profis, with the help of cardiologist Jon Saroff of Kaiser Permanente medical center in San Francisco compared various wrist monitor brands with the gold standard EKG measurements, and found them well off-beam especially at over 100 bpm. However, the Garmin Vivofit chest strap monitor, which measures electrical activity, was very accurate. This device can be bought for around $150 in Australia.

3. Cholesterol

Cholesterol’s an essential organic molecule, a sterol, a structural component of our cell membranes. It’s biosynthesised, mainly by our liver cell, often as a precursor to such vital entities as steroid hormones and vitamin D, and researchers have tracked the 37-step process of its synthesis. Cholesterol is transported through the blood within lipoproteins, and that’s where you get HDL (high-density lipoprotein) and LDL (low-density lipoprotein) cholesterol, of which the former is the one that causes problems. Some 32% of Australian adults have high blood cholesterol, the primary cause of atherosclerosis, leading to clogging of major blood vessels. Ways of lowering your LDL levels include not smoking, avoiding transfats, regular moderate exercise, and healthy eating including fruit, veg, grains and pulses and sterol-enriched foods. But of course you know all that. The big question is, can you measure your cholesterol from home? The current answer appears to be no, according to the Harvard Medical School (though I note that their article is 11 years old). The problem is that home testing kits can’t separate the ‘good’ HDL cholesterol from the ‘bad” (LDL). Measuring your overall cholesterol levels might be useful, but the real issue is the proportion that is LDL, not to mention that cholesterol can also be carried by other molecules such as triglycerides.

 4. Blood sugar/glucose

Glucose is a vital source of energy for the body’s cells, and its levels are associated with the hormone insulin, produced by the pancreas. Blood glucose levels naturally vary throughout the day, and having a level regularly above normal is termed hyperglycemia. Hypoglycemia is the term for low levels. Diabetes (technically Diabetes mellitus) is the disease most commonly associated with high blood sugar. General symptoms are frequent urination, hunger pangs and increased thirst.  The mean normal blood sugar level is around 5.5 mM (millimolars). That’s the international standard measure – the Americans measure it differently, which causes the usual confusion. Not surprisingly, considering the global rise in diabetes, blood glucose meters for use at home are readily available, but they’re mostly specially devised for use by diabetics, supervised by healthcare professionals. You can of course buy one and DIY but you must learn to be inured to pricks, and unless you’re at risk, which I’m not, as I don’t have much of a sweet tooth, don’t have particularly high cholesterol, and have never evinced any diabetic symptoms, it’s probably not worth the investment. The essential test associated with ‘pre-diabetes’ or hypoglycaemia is a glucose-tolerance test (GTT).

5. Sequence your genome

According to the Australian government’s National Health and Medical Research Council (NHMRC):

Rapid advances in DNA sequencing technologies now allow an individual’s whole genome to be sequenced. Although this is still relatively expensive, it is likely that in the near future it will become affordable and readily available.

Ah, that other country, the near future. But it is a fact that the price is coming down, from $10 million in 2005 to a mere $1 million in 2007 when James Watson’s genome was sequenced. The going rate in 2012 was under $10,000, and this year (2014) the Garvan Institute of Medical Research in Sydney became one of only three institutes in the world to deliver whole sequenced genomes at under $1000. However, there’s a problem. Your genome will mean nothing to you without expert analysis and interpretation, at a hefty price tag. So what would be the purpose, from a health perspective, of ‘doing your genome’? If you’re already quite healthy, do you want to spend up to $1000 only to find out that you carry a gene which may pre-dispose you to a disease that’s currently non-preventable? Our genome is very complex, so much so that current thinking on the subject, and especially on the introns, the sections that don’t code for proteins, has become more cloudy than ever. We know, or think we know, that the number of introns an organism has is positively correlated with that organism’s complexity, but that’s about all we know for sure, and  considering the enormous complexity of the interaction between genetics and environment, together with our lack of knowledge of the role of so much of our genome (over 98% of which is non-coding DNA), the question of whether it’s worth sequencing at this time is a live one. Of course if the price comes down to $100, or the price of a latte (which will soon be up around that figure) then it’d be well worth it; you would have it there awaiting scientific breakthroughs on all that non-coding stuff.

6. microbiome

If you’ve been paying attention to the world of human health, you’ll know that the microbiome is all the rage at the moment. the term was coined by Joshua Lederburg, who defined it thus, according to Wikipedia:

A microbiome is “the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space.”

You may well have heard the impressive statistic that you have ten times more bacterial cells (and, most interestingly, archaean cells) growing on or in you than bodily (eukaryotic) cells, though this might become less impressive when you learn that the combined weight of those cells amounts to only a few hundred grams. Still, recent research on the microbiota has turned up some interesting results, especially for health. One finding, which may make it difficult to assess your own microbiome, is that different sets of microbes appear to perform the same function for different people. So you won’t just need to know the genetic content of your microbiome, but its function. Still, we can learn a lot already from our microbiome, according to Catalyst, the ABC science program. For example, we inherit a lot of bacteria from our mothers, via her breast milk, not only directly but because the sugars in breast milk encourage the growth of particular types of bacteria. Most of this gut bacteria does its work in the large intestine or bowel region. They’re anaerobic beasties, so they die when exposed to air. However, recent technological developments (and how often can that story be told) have allowed us to learn far more about them, by sequencing their genes inside the gut. From this we’ve learned that our gut bacteria are vital components of our immune system. And since these bacteria rely on our own diets for their nourishment, the kind of microbiome we have is profoundly related to what we eat. A diverse microbiome results, apparently, from eating a high-fibre diet, and low-fibre processed food, and the ingesting of antibiotics, is reducing that diversity, and contributing to multiple health problems. It appears that a less diverse microbiome finds itself under stress, leading to inflammation, an immune response that can damage our own tissue. As a sufferer from bronchiectasis, a chronic (and incurable) inflammation of the airways due probably to early childhood damage, I’m particularly concerned to limit the extent of inflammation through diet and exercise, so this is probably the aspect of my health I’m most concerned to monitor. And there’s also the relationship between gut bacteria and obesity. Some 62% of Australians are overweight or obese, and I’m one of that majority, and trying not to be.

It has been shown clearly, in mice at least, that a high-fibre diet reduces bronco-constriction, improving resistance to asthma and other airways conditions such as COPD. This is mainly due to the production of short-chain fatty acids by particular bacteria. The short-chain fatty acids are produced though the digestion of dietary fibre. Interestingly, acetate, found in vinegar, is a short-chain fatty acid, and a natural anti-inflammatory, so that’s something I should include regularly in my diet.

Finding out what your particular microbiome is, and how it might align with your health, is a simple if rather unpalatable and ‘intimate’ process. You can apply for a kit from the American Gut Project, an organisation dedicated to researching microbiota. The kit is for obtaining a sample of your ‘biomass’ as they call it, which you then send back to the AGP for analysis. All of this was spelt out in the above-linked Catalyst program, but since that program was aired two months ago, the AGP has been inundated with more biomass than it can deal with, so there’s been a backlog of logs, as it were. I plan to send for a kit anyway. The AGP sends back the results, apparently, with hopefully an analysis of the microbiome easy enough for a layperson to understand.


So there’s six areas to look at, either independently or with the help of your GP or other professionals, in terms of measuring how you’re going in terms of overall health, and there are many more aspects of your bodily chemistry and physiology to check up on – hormones, neurotransmitters, bone density, sight, hearing, lung capacity and so forth. Or you can follow the standard advice on diet and exercise, try to avoid stress and hope for the best. And above all don’t stop laughing and dancing, otherwise life would hardly be worth living.

Written by stewart henderson

November 1, 2014 at 6:36 pm