Source: BiochemFFA_6_4.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Sugars are the building blocks of carbohydrates, amino acids are the building blocks of proteins and nucleotides are the building blocks of the nucleic acids - DNA and RNA. Another crucial building block is acetyl-CoA, which is used to build many lipid substances, including fatty acids, cholesterol, fat soluble vitamins, steroid hormones, prostaglandins, endocannabinoids, and the bile acids. Indeed, acetyl-CoA goes into more different classes of molecule than any other building block.
We focus our attention here on a group of molecules made from acetyl-CoA that are known as as the isoprenoids. Isoprenoids are a large, diverse and ancient group of molecules that are found in all three domains of life. As noted earlier, they are components of membrane lipids in the cell membranes of archaebacteria, but beyond this, they serve an astonishing variety of functions. From photosynthetic pigments to plant defense compounds, from flavor compounds in cinnamon, mint, ginger and cloves to plant and animal hormones, from the cannabinoids in marijuana to the lycopene that gives tomatoes their color, and from heme to the quinones in the electron transport chain, isoprenoids are ubiquitous in cells. Isoprenoids derive their name from the fact that they are, in fact, made from five carbon building blocks called isoprenes that are derived from acetyl-CoA. The synthesis of the two isoprene units - isopentenyl pyrophosphate and dimethylallyl pyrophosphate is shown in Figure 6.111 and Figure 6.112.
The pathway leading up to isoprene synthesis overlaps with that of ketone body synthesis, for the two reactions (Figure 6.112), as has been discussed earlier in this book (see HERE). Thiolase catalyzes the initial reaction, joining together two acetyl-CoA molecules to make acetoacetyl-CoA. In the second reaction catalyzed by HMG-CoA synthase, a third acetyl-CoA is joined to form the six carbon compound known as hydroxymethyl glutaryl-CoA (HMG-CoA). Reaction three is an important one biologically and medically because of the enzyme catalyzing it - HMG-CoA reductase.
Medically, HMG-CoA reductase is the target of a class of drugs known as statins (Figure 6.113 & Movie 6.1), which are used to reduce cholesterol levels in people. These competitive inhibitors, which compete with HMG-CoA for binding have two effects. First, they reduce the production of mevalonate, which restricts the amount of substrate available to make cholesterol. Second, and perhaps more importantly, they increase production of LDL receptors in the liver, which favors uptake and destruction of LDLs, thus lowering serum cholesterol levels.
Biologically, the HMG-CoA reductase enzyme is also of importance because it is the primary regulatory point in cholesterol synthesis. Control of it is complex. First, it is feedback inhibited by cholesterol itself. High levels of glucose in the blood activate the enzyme. Phosphorylation by AMP-activated protein kinase inhibits its activity. Interestingly, the same enzyme phosphorylates and inactivates acetyl-CoA carboxylase - the only regulatory enzyme controlling fatty acid synthesis. Transcription of the gene encoding HMG-CoA reductase
is enhanced by binding of the sterol regulatory element binding protein (SREBP) to the sterol recognition element (SRE ) located near the gene coding sequence. As cholesterol levels rise, SREBP is proteolytically cleaved and transcription stops.
From HMG-CoA, the enzyme HMG-CoA reductase catalyzes the formation of mevalonate. This reaction requires NADPH and results in release of coenzyme A. Mevalonate gets phosphorylated twice and then decarboxylated to yield the five carbon intermediate known as isopentenyl-pyrophosphate (IPP). IPP is readily converted to the other important isoprenoid unit, dimethylallylpyrophosphate (DMAPP).
These two five carbon compounds, IPP and DMAPP, are also called isoprenes (Figure 6.115) and are the building blocks for the synthesis of cholesterol and related compounds. This pathway proceeds in the direction of cholesterol starting with the joining of IPP and DMAPP to form geranyl-pyrophosphate. Geranyl-pyrophosphate combines with another IPP to make farnesyl-pyrophosphate, a 15-carbon compound.
Two farnesyl-pyrophosphates join to create the 30-carbon compound known as squalene. Squalene, in a complicated rearrangement involving reduction and molecular oxygen forms a cyclic intermediate known as lanosterol (Figure 6.116) that resembles cholesterol. Conversion of lanosterol to cholesterol is a lengthy process involving 19 steps that occur in the endoplasmic reticulum.
The cholesterol biosynthesis pathway from lanosterol is a long one and requires significant amounts of reductive and ATP energy. As noted earlier (see HERE), cholesterol has an important role in membranes. It is also a precursor of steroid hormones and bile acids and its immediate metabolic precursor, 7-dehydrocholesterol (Figure 6.117), branches to form vitamin D (Figure 6.118).
All steroid hormones in animals are made from cholesterol and include the progestagens, androgens, estrogens, mineralocorticoids, and the glucocorticoids. The branch molecule for all of the steroid hormones is the cholesterol metabolite (and progestagen) known as pregnenalone (Figure 6.119). The progestagens are thus precursors of all of the other classes of steroid hormones.
The estrogens are derived from the androgens in an interesting reaction that required formation of an aromatic ring (Figure 6.120). The enzyme catalyzing this reaction is known as an aromatase and it is of medical significance. The growth of some tumors is stimulated by estrogens, so aromatase inhibitors are prescribed to prevent the formation of estrogens and slow tumor growth. Two commonly used inhibitors include exemestane (a suicide inhibitor - Figure 6.121) and anastrozole (a competitive inhibitor).
Other fat-soluble vitamins
Synthesis of other fat soluble vitamins and chlorophyll also branches from the isoprenoid synthesis pathway at geranyl pyrophosphate. Joining of two geranylgeranyl pyrophosphates occurs in plants and bacteria and leads to synthesis of lycopene, which, in turn is a precursor of β-carotene, the final precursor of Vitamin A (see below also). Vitamins E and K, as well as chlorophyll are all also synthesized from geranylgeranyl pyrophosphate.
Bile acid metabolism
Another metabolic pathway from cholesterol leads to the polar bile acids, which are important for the solubilization of dietary fat during digestion. Converting the very non-polar cholesterol to a bile acid involves oxidation of the terminal carbon on the side chain off the rings. Other alterations to increase the polarity of these compounds include hydroxylation of the rings and linkage to other polar compounds.
Common bile acids include cholic acid, chenodeoxycholic acid, glycocholic acid, taurocholic acid, and deoxycholic acid (Figure 6.123). Another important consideration about bile acids is that their synthesis reduces the amount of cholesterol available and promotes uptake of LDLs by the liver. Normally bile acids are recycled efficiently resulting in limited reduction of cholesterol levels. However, inhibitors of the recycling promote reduction of cholesterol levels.
Vitamin A Synthesis
Vitamin A is important for many cellular functions related to growth, differentiation and organogenesis during embryonic development, tissue maintenance, and vision, to name a few.
There are three main active forms of the vitamin, retinal, retinol and retinoic acid, each with its own set of functions. Retinal, complexed with the protein, opsin, is found in the rod cells of the retina and is necessary for vision. Retinol and retinoic acid both function as signaling molecules that can modulate gene expression during development.
Synthesis of vitamin A occurs as a branch in synthesis of isoprenoids. Addition of isopentenyl pyrophosphate to farnesyl pyrophosphate creates a 20-carbon intermediate, geranylgeranyl pyrophosphate (GGPP - Figure 6.124).
Joining of two GGPPs creates a 40 carbon intermediate that is unstable and decomposes to phytoene. Desaturases oxidize two single bonds in phytoene, creating lycopene.
Lycopene is a linear 40 carbon unsaturated molecule found in tomatoes and other red vegetables and it gives them their color. Cyclization of end portions of lycopene give rise to β-carotene, the precursor of vitamin A (retinal/retinol - Figure 6.124).
β-carotene is found in carrots and other orange vegetables, and is converted in the body to vitamin A. Catalytic action by β-Carotene 15,15’ monooxygenase cleaves β-carotene to form retinal (the aldehyde form used in vision).
The enzyme retinol dehydrogenase catalyzes reduction of retinal to retinol (storage form). Oxidation of retinal creates another important retinoid known as retinoic acid. This form of vitamin A cannot be reduced back to retinal and thus cannot be used for vision or storage.
Instead, retinoic acid has roles in embryonic development. Retinoic acid acts through binding to the Retinoic Acid Receptor (RAR). RAR binds to DNA and affects transcription of several important sets of genes important for differentiation. These include the Hox genes, which control anterior/posterior patterning in early embryonic development.
Synthesis of sphingolipids, which are found primarily in brain and nerve tissue, begins with palmitoyl-CoA and serine that combine to make an 18-carbon amine called 3-keto-sphinganine (Figure 6.125). Reduction of that by NADPH yields dihydrosphingosine and addition of a fatty acid from an acyl-CoA yields N-acylsphinganine, which is a ceramide (Figure 6.126). A ceramide can be converted into a cerebroside by addition of a glucose from UDP-glucose (Figure 6.127).
If a few other simple sugars are added to the cerebroside, a globoside is created. If, instead of adding sugar, a phosphocholine is added from phosphatidylcholine, then sphingomyelin is created (Figure 6.127). If a complex set of sugars are added to to a cerebroside, then a ganglioside results (Figure 6.127).
In the overall metabolism of sphingolipids, the greatest problems arise with their catabolism. Figure 6.128 illustrates the numerous genetic diseases arising from mutations in DNA coding for some of these enzymes. All are lysosomal storage diseases and many of these are quite severe. GM1 glandiosidoses (arising from inability to breakdown GM1 gangliosides) cause severe neurodegeneration and seizures. Individuals suffering from them typically die by age 3. Tay-Sachs disease usually causes death by age 4, though late-onset forms of the disease in adults are known.
With Gaucher’s disease, three different types have been described with widely varying effects. In some, the disease is fatal by age four and in others, it does not manifest until teens or even adulthood. Fabry’s disease patients can live into their 50s, on average.
Glycerophospholipids are the major components of membranes. Synthesis of glycerophospholipids begins with glycerol-3-phosphate. In the first reaction, glycerol-3-phosphate gains a fatty acid at position one from an acyl-CoA, followed by a duplicate reaction at position two to make phosphatidic acid (Figure 6.129). This molecule, which can branch to other reactions to form fats, is an important intermediate in the synthesis of many glycerophospholipids. Glycerophospholipid compounds can often be made by more than one pathway. The nucleotide CDP plays an important role in glycerophospholipid synthesis, serving as part of an activated intermediate for synthesis of phosphatidyl compounds. This is necessary, because formation of the phosphodiester bonds of these compounds requires higher energy input.
Cells use two strategies to accomplish this. Both involve CDP. In the first, CTP combines with phosphatidic acid to make CDP-diacylglcyerol with release of a pyrophosphate. The reaction is catalyzed by phosphatidate cytidylyltransferase.
CDP-diacylglycerol then serves as an activated intermediate to donate the phosphotidate part of itself to another molecule. The reaction below illustrates one example
The second strategy is to make a CDP derivative of the group being added to phosphatidic acid. An example is shown next
Then the CDP donates the phosphocholine to a diacylglycerol to made phosphatidylcholine and CMP
Synthesis of other important glycerophospholipids follows from these basic strategies. Phosphatidylethanolamine can be easily made from phosphatidylserine by decarboxylation.
Phosphatidylethanolamine can serve as a precursor in an alternative pathway for making phosphatidylcholine (SAM = S-Adenosyl Methioinine / SAH = S-Adenosyl Homocysteine)
Phosphatidylserine and phosphatidylethanolamine can swap groups reversibly in the reaction below
Similarly, phosphatidylserine and phosphatidylcholine can be interchanged as follows:
Phosphatidylglycerol can be made from glycerol-3-phosphate and CDP-diacylglycerol
Cardiolipin, which is essentially a diphosphatidyl compound can be made by joining CDP-diacylglyerol with phosphatidylglycerol
Phosphtidylinositol can be made from CDP-diacylglycerol and inositol .
The porphyrin ring found in the hemes of animals, fungi, and protozoa (Figure 6.130) is synthesized starting from very simple compounds (Figure 6.131). The process is a bit complicated, occurring between the cytoplasm and the mitochondrion. The first step is the creation of δ-aminolevulinic acid (also called aminolevulinic acid or dALA) from glycine and Succinyl-CoA.
Joining of two δ-aminolevulinic acid molecules together with splitting out of two molecules of water yields porphobilinogen.
Joining of four molecules of porphobilinogen together yields hydroxylmethylbilane (Figure 6.132).
Next, a series of reactions involving 1) loss of water; 2) loss of four molecules of carbon dioxide; 3) loss of two more carbon dioxides, loss of six protons and electrons and (finally) 4) addition of Fe++ with loss of two protons yields heme. Individual heme molecules may be further processed.
Two enzymes in heme synthesis are sensitive to the presence of lead, and this is one of the primary causes of lead toxicity in humans. Inhibition of the enzymes leads to 1) anemia and 2) accumulation of δ-aminolevulinic acid, which can be harmful to neurons in development, resulting in learning deficiencies in children.
Defects in enzymes of the pathway can also lead to porphyrias, diseases in which one or more of the intermediates in the heme synthesis pathway accumulate due to deficiency of the enzyme necessary to convert the accumulating material into the next molecule in the pathway. The accumulation of purplish intermediates gave the diseases the name porphyria from the Greek word for purple.
Severe porphyrias can lead to brain damage, nerve damage, and mental disturbances. The “madness” of King George III may have been due to a form of porphyria. In other manifestations of the disease, cutaneous porphyrias cause skin problems on exposure to light. This need, for patients with certain forms of porphyria, to avoid light, coupled with the fact that porphyrias can be treated by blood tranfusions, may have led to the legend of vampires.
Breakdown of heme
Catabolism of heme (Figure 6.133) begins in macrophages within the spleen . Targets for degradation are hemes within damaged red blood cells, which get removed from the blood supply due to their appearance. It is because of this system, for example, that sickle cell anemia is classified as an anemia (decrease in red blood cells or hemoglobin in the blood). After cells have sickled, they lose their shape and are more likely to be removed from the blood by this process, leaving the patient weakened from low blood cell counts.
The first biochemical step in catabolism is conversion of heme to biliverdin. This reaction is catalyzed by heme oxygenase and requires electrons from NADPH. In the process, Fe++ is released. Interestingly, carbon monoxide is also produced and it acts as a vasodilator.
Next, biliverdin is converted to bilirubin by biliverdin reductase and is secreted from the liver into bile. Bacteria in the intestine convert bilirubin to urobilinogens, some of which is absorbed intestinal cells and transported into kidneys and excreted. The yellow color of urine arises from the compound known as urobilin, which is an oxidation product of urobilinogen. The remainder of the urobilinogens are converted in the intestinal tract to stercobilinogen whose oxidation product is stercobilin and it gives the color associated with feces.