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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 Study.com:

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.

References

Cholesterol biosynthesis part 1, by Ben1994, 2015

Cholesterol biosynthesis part 2, by Ben 1994, 2015

https://www.britannica.com/science/ketone

http://www.phschool.com/science/biology_place/biocoach/bioprop/ribose.html

https://en.wikipedia.org/wiki/Acetyl-CoA

https://study.com/academy/lesson/mitochondrial-matrix-definition-function-quiz.html

https://www.khanacademy.org/science/biology/cellular-respiration-and-fermentation/oxidative-phosphorylation/a/oxidative-phosphorylation-etc

Written by stewart henderson

October 14, 2019 at 5:26 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.

References

https://en.wikipedia.org/wiki/Mevalonate_pathway

https://cosmosmagazine.com/society/will-statin-day-really-keep-doctor-away

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

Cholesterol structure, part 1/2, by Catalyst University

https://en.wikipedia.org/wiki/Cholesterol

https://en.wikipedia.org/wiki/Statin

https://en.wikipedia.org/wiki/Lipoprotein

https://en.wikipedia.org/wiki/Saturated_fat

Written by stewart henderson

September 15, 2019 at 10:24 am