The amazing fatty acid synthase nano factories, and origin of life scenarios

The amazing fatty acid synthase nano factories, and origin of life scenarios

https://reasonandscience.catsboard.com/t2168-the-amazing-fatty-acid-synthase-nano-factories-and-origin-of-life-scenarios

Lipids (‘fats’) are essential for the formation of a cell membrane that contains the cell contents, as well as for other cell functions. The cell membrane, comprised of several different complex lipids, is an essential part of a free-living cell that can reproduce itself. 4

Lipids have much higher energy density than sugars or amino acids, so their formation in any chemical soup is a problem for origin of life scenarios (high energy compounds are thermodynamically much less likely to form than lower energy compounds).

The fatty acids that are the primary component of all cell membranes have been very difficult to produce, even assuming the absence of oxygen (a ‘reducing’ atmosphere). Even if such molecules were produced, ions such as magnesium and calcium, which are themselves necessary for life and have two charges per atom (++, i.e. divalent), would combine with the fatty acids, and precipitate them, making them unavailable.

Biological lipids are a chemically diverse group of compounds, the common and defining feature of which is their insolubility in water. The biological functions of the lipids are as diverse as their chemistry. Fats and oils are the principal stored forms of energy in many organisms. Phospholipids and sterols are major structural elements of biological membranes. Other lipids, although present in relatively small quantities, play crucial roles as enzyme cofactors, electron carriers, light-absorbing pigments, hydrophobic anchors for proteins, “chaperones” to help membrane proteins fold, emulsifying agents in the digestive tract, hormones, and intracellular messengers.  

Lipids play a variety of cellular roles, some only recently recognized. They are the principal form of stored energy in most organisms and major constituents of cellular membranes. Specialized lipids serve as

pigments (retinal, carotene)
cofactors (vitamin K)
detergents (bile salts)
transporters (dolichols)
hormones (vitamin D derivatives, sex hormones)
extracellular and intracellular messengers (eicosanoids, phosphatidylinositol derivatives)
anchors for membrane proteins (covalently attached fatty acids, prenylgroups, and phosphatidylinositol)

Storage Lipids

The fats and oils used almost universally as stored forms of energy in living organisms are derivatives of fatty acids. The fatty acids are hydrocarbon derivatives, at about the same low oxidation state (that is, as highly reduced) as the hydrocarbons in fossil fuels. The cellular oxidation of fatty acids (to CO2 and H2O), like the controlled, rapid burning of fossil fuels in internal combustion engines, is highly exergonic.

Among the most biologically significant properties of lipids are their hydrophobic properties. These properties are mainly due to a particular component of lipids: fatty acids, or simply fats. Fatty acids are hydrocarbon chains of various lengths and degrees of unsaturation that terminate with a carboxylic acid group. The fatty acid chains in membranes usually contain between 14 and 24 carbon atoms; they may be saturated or unsaturated. Short chain length and unsaturation enhance the fluidity of fatty acids and their derivatives by lowering the melting temperature.

Structural Lipids in Membranes

The central architectural feature of biological membranes is a double layer of lipids, which acts as a barrier to the passage of polar molecules and ions. Membrane lipids are amphipathic: one end of the molecule is hydrophobic, the other hydrophilic. Their hydrophobic interactions with each other and their hydrophilic interactions with water direct their packing into sheets called membrane bilayers.

Storage Lipids
■ Lipids are water-insoluble cellular components, of diverse structure, that can be extracted by nonpolar solvents.
■ Almost all fatty acids, the hydrocarbon components of many lipids, have an even number of carbon atoms (usually 12 to 24); they are either saturated or unsaturated, with double bonds almost always in the cis configuration.
■ Triacylglycerols contain three fatty acid molecules esterified to the three hydroxyl groups of glycerol. Simple triacylglycerols contain only one type of fatty acid; mixed triacylglycerols, two or three types. Triacylglycerols are primarily storage fats; they are present in many foods.
■ Partial hydrogenation of vegetable oils in the food industry converts some cis double bonds to the trans configuration. Trans fatty acids in the diet are an important risk factor for coronary heart disease.

There are five general types of membrane lipids:
■ Glycerophospholipids, in which the hydrophobic regions are composed of two fatty acids joined to glycerol; galactolipids and sulfolipids, which also contain two fatty acids esterified to glycerol, but lack the characteristic phosphate of phospholipids
■ Archaeal tetraether lipids, in which two very long alkyl chains are ether-linked to glycerol at both ends; sphingolipids, in which a single fatty acid is joined to a fatty amine
■ Sphingosine and sterols, compounds characterized by a rigid system of four fused hydrocarbon rings.
■ The polar lipids, with polar heads and nonpolar tails, are major components of membranes. The most abundant are the glycerophospholipids, which contain fatty acids esterified to two of the hydroxyl groups of glycerol, and a second alcohol, the head group, esterified to the third hydroxyl of glycerol via a phosphodiester bond. Other polar lipids are the sterols.

Glycerophospholipids differ in the structure of their head group; common glycerophospholipids are phosphatidylethanolamine and phosphatidylcholine. The polar heads of the
glycerophospholipids are charged at pH near 7.
Chloroplast membranes are rich in galactolipids, composed of a diacylglycerol with one or two linked galactose residues, and sulfolipids, diacylglycerols with a linked sulfonated sugar residue and thus a negatively charged head group.
Archaea have unique membrane lipids, with long-chain alkyl groups ether-linked to glycerol at both ends and with sugar residues and/or phosphate joined to the glycerol to provide a polar or charged head group. These lipids are stable under the harsh conditions in which archaea live.

The sphingolipids contain sphingosine, a long-chain aliphatic amino alcohol, but no glycerol. Sphingomyelin has, in addition to phosphoric acid

Lipids as Signals,Cofactors,and Pigments

The two functional classes of lipids considered thus far (storage lipids and structural lipids) are major cellular components; membrane lipids make up 5% to 10% of the dry mass of most cells, and storage lipids more than 80% of the mass of an adipocyte. With some important exceptions, these lipids play a passive role in the cell; lipid fuels are stored until oxidized by enzymes, and membrane lipids form impermeable barriers around cells and cellular compartments. Another group of lipids, present in much smaller amounts, have active roles in the metabolic traffic as metabolites and messengers. Some serve as potent signals—as hormones, carried in the blood from one tissue to another, or as intracellular messengers generated in response to an extracellular signal (hormone or growth factor). Others function as enzyme cofactors in electron-transfer reactions in chloroplasts and mitochondria, or in the transfer of sugar moieties in a variety of glycosylation reactions. A third group consists of lipids with a system of conjugated double bonds: pigment molecules that absorb visible light. Some of these act as light-capturing pigments in vision and photosynthesis; others produce natural colorations, such as the orange of
pumpkins and carrots and the yellow of canary feathers. Finally, a very large group of volatile lipids produced in plants serve as signals that pass through the air, allowing
plants to communicate with each other, and to invite animal friends and deter foes. We describe in this section a few representatives of these biologically active lipids. In
later chapters, their synthesis and biological roles are considered in more detail.

Some types of lipids, although present in relatively small quantities, play critical roles as cofactors or signals.
■ Phosphatidylinositol bisphosphate is hydrolyzed to yield two intracellular messengers, diacylglycerol and inositol 1,4,5-trisphosphate. Phosphatidylinositol 3,4,5-trisphosphate is a nucleation point for supramolecular protein complexes involved in biological signaling.
■ Prostaglandins, thromboxanes, and leukotrienes (the eicosanoids), derived from arachidonate, are extremely potent hormones.
■ Steroid hormones, derived from sterols, serve as powerful biological signals, such as the sex hormones.
■ Vitamins D, A, E, and K are fat-soluble compounds made up of isoprene units. All play essential roles in the metabolism or physiology of animals. Vitamin D is precursor to a hormone that regulates calcium metabolism. Vitamin A furnishes the visual pigment of the vertebrate eye and is a regulator of gene expression during epithelial cell growth. Vitamin E functions in the protection of membrane lipids from oxidative damage, and vitamin K is essential in the blood-clotting process.
■ Ubiquinones and plastoquinones, also isoprenoid derivatives, are electron carriers

The ability to synthesize a variety of lipids is essential to all organisms. It will be described the biosynthetic pathways for some of the most common cellular lipids, illustrating the strategies employed in assembling these water-insoluble products from water-soluble precursors such as acetate. Like other biosynthetic pathways, these reaction sequences are endergonic and reductive. They use ATP as a source of metabolic energy and a reduced electron carrier (usually NADPH) as a reductant. We first describe the biosynthesis of fatty acids, the primary components of both triacylglycerols and phospholipids, then examine the assembly of fatty acids into triacylglycerols and the simpler membrane phospholipids. 

Lipid Synthesis

Synthesis of most lipids in microorganisms can be viewed as having two essential components—fatty acid synthesis and glycerol synthesis. Synthesis starts with transfer of the acetyl group of acetyl-CoA to a carrier protein called acyl carrier protein (ACP). This carrier serves to hold the fatty acid chain as it is elongated by progressively adding 2-carbon units. When the newly synthesized fatty acid reaches its requiredlength, usually 14, 16, or 18 carbons long, it is released from ACP. The glycerol component of the fat is synthesized from dihydroxyacetone phosphate.



Fatty Acids

Fatty acids are important for energy storage, phospholipid membrane formation, and signaling pathways. Fatty acid metabolism consists of catabolic processes that generate energy and primary metabolites from fatty acids, and anabolic processes that create biologically important molecules from fatty acids and other dietary sources.3

Fatty acid synthesis is the creation of fatty acids from acetyl-CoA and malonyl-CoA precursors through action of enzymes called fatty acid synthases. It is an important part of the lipogenesis process, which – together with glycolysis – functions to create fats from blood sugar in living organisms. 1

The synthesis of long-chain fatty acids (lipogenesis) is carried out by two enzyme systems: acetyl-CoA carboxylase and fatty acid synthase.

Fatty acids are essential nutrients for all organisms, except archaea. 2 A fatty acid is a carboxylic acid with a long, unbranched aliphatic tail that is either saturated or unsaturated.

Within cells, fatty acids serve many vital functions:

·        As major components of cell membranes, including internal organelle membranes (each phospholipid contains two fatty acid tails)
·        For  energy storage - (yields significantly more energy than carbohydrates, for the same mass)
·        As messenger substances (e.g. ceramide is a fatty acid-containing messenger in cytokine-induced apoptosis)
·        For the post-translational modification of certain proteins
The synthesis of fatty acids is essentially the reverse chemistry of its degradation by oxidation, both pathways involving an activated two-carbon intermediate, acetyl-CoA.  Therefore, a cell needs a means of separating the two opposing pathways in order to allow their independent control.  In eukaryotes, this is achieved both physically and chemically:
·        Fatty acid synthesis occurs in the cytoplasm, while its oxidation occurs in mitochondria
·        Fatty acid synthesis requires the oxidation of the co-factor NADPH, while fatty acid oxidation requires the reduction of FAD+ and NAD+
In addition, distinct enzymes control the two pathways, permitting a further level of control.  Fatty acid synthesis is carried out by fatty acid synthase.

Fatty Acids Are Hydrocarbon Derivatives

Fatty acids are carboxylic acids with hydrocarbon chains ranging from 4 to 36 carbons long (C4 to C36). In some fatty acids, this chain is unbranched and fully saturated (contains no double bonds); in others the chain contains one or more double bonds ( See picture below ). A few contain three-carbon rings, hydroxyl groups, or methylgroup branches. At room temperature (25 C), the saturated fatty acids from 12:0 to 24:0 have a waxy consistency, whereas unsaturated fatty acids of these lengths are oily liquids. This difference in melting points is due to different degrees of packing of the fatty acid molecules. In the fully saturated compounds, free rotation around each carbon–carbon bond gives the hydrocarbon chain great flexibility; the most stable conformation is the fully extended form, in which the steric hindrance of neighboring atoms is minimized. These molecules can pack together tightly in nearly crystalline arrays, with atoms all along their lengths in van der Waals contact with the atoms of neighboring molecules. In unsaturated fatty acids, a cis double bond forces a kink in the hydrocarbon chain. Fatty acids with one or several such kinks cannot pack together as tightly as fully saturated fatty acids, and their interactions with each other are therefore weaker. Because less thermal energy is needed to disorder these poorly ordered arrays of unsaturated fatty acids, they have markedly lower melting points than saturated fatty acids of the same chain length.



The most commonly occurring fatty acids have even numbers of carbon atoms in an unbranched chain of 12 to 24 carbons . the even number of carbons results from the mode of
synthesis of these compounds, which involves successive condensations of two-carbon (acetate) units.

Fatty acids are carboxylic acids with hydrocarbon chains ranging from 4 to 36 carbons long (C4 to C36). In some fatty acids, this chain is unbranched and fully saturated (contains no double bonds); in others the chain contains one or more double bonds . A few contain three-carbon rings, hydroxyl groups, or methylgroup branches.




Fatty acid synthesis

 a

The input to fatty acid synthesis is acetyl-CoA, which is carboxylated to malonyl-CoA. The ATP-dependent carboxylation   provides energy input. The CO2 is lost later during condensation with the growing fatty acid. The spontaneous decarboxylation drives the condensation.

Fatty acid synthesis is the creation of fatty acids from acetyl-CoA and malonyl-CoA precursors through action of enzymes called fatty acid synthases. It is an important part of the lipogenesis process, which – together with glycolysis – functions to create fats from blood sugar in living organisms. 1

The Reaction Sequence for the Biosynthesis of Fatty Acids

Biosynthesis of Fatty Acids and Eicosanoids

After the discovery that fatty acid oxidation takes place by the oxidative removal of successive two-carbon (acetyl-CoA) units, biochemists thought the biosynthesis of fatty acids might proceed by a simple reversal of the same enzymatic steps. However, as they were to find out, fatty acid biosynthesis and breakdown occur by different pathways, are catalyzed by different sets of enzymes, and take place in different parts of the cell. Moreover, biosynthesis requires the participation of a three-carbon intermediate,
malonyl-CoA, that is not involved in fatty acid breakdown.

The first step : 

Malonyl-CoA Is Formed from Acetyl-CoA and Bicarbonate

The formation of malonyl-CoA from acetyl-CoA is an irreversible process, catalyzed by acetyl-CoA carboxylase. The bacterial enzyme has three separate polypeptide subunits;


The acetyl-CoA carboxylase reaction. Acetyl-CoA carboxylase has three functional regions: biotin carrier protein (gray); biotin carboxylase, which activates CO2 by attaching it to a nitrogen in the biotin ring in an ATP-dependent reaction; and transcarboxylase, which transfers activated CO2 (shaded green) from biotin to acetyl-CoA, producing malonyl-CoA. The long, flexible biotin arm carries the activated CO2 from the biotin carboxylase region to the transcarboxylase active site. The active enzyme in each step is shaded blue.


In animal cells, all three activities are part of a single multifunctional polypeptide. Plant cells contain both types of acetyl- CoA carboxylase. In all cases, the enzyme contains a
biotin prosthetic group covalently bound in amide linkage to the e-amino group of a Lys residue in one of the three polypeptides or domains of the enzyme molecule. The two-step reaction catalyzed by this enzyme is very similar to other biotin-dependent carboxylation reactions, such as those catalyzed by pyruvate carboxylase  and propionyl-CoA carboxylase . A carboxyl group, derived from bicarbonate (HCO3 ), is first transferred to biotin in an ATP-dependent reaction. The biotinyl group serves as a temporary carrier of CO2, transferring it to acetyl-CoA in the second step to yield malonyl-CoA.

The second step:


Fatty acid synthase 

Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery. Fatty acid synthases resemble an iterative assembly line, with an acyl carrier protein conveying the growing fatty acid to necessary enzymatic domains for modification. Each catalytic domain is a unique enzyme spanning a wide range of folds and structures. Although they harbor the same enzymatic activities, two different types of fatty acid synthase architectures are observed in nature. 5


A battery of enzymes are required to synthesise fatty acids, however their organisation differs among species.  Fatty acid synthetase (FAS) can be divided into two groups based on the organisation of their catalytic units: fatty acid synthase I (FAS I), found in vertebrates and fungi, and fatty acid synthase II (FAS II), found in plants and bacteria. The FAS I found in vertebrates consists of a single multifunctional polypeptide chain. The mammalian FAS I is the prototype. Seven active sites for different reactions lie in separate domains. 


Type I FAS systems

Type I FAS systems are multi-enzyme complexes that contain all the catalytic units as distinct domains covalently linked into one (alpha) or two (alpha and beta) polypeptides.  Type I systems include eukaryotic, as well as a few bacterial, FAS enzymes.  These systems can be further divided into subgroups according to the organisation of individual polypeptides and the domains within these polypeptides:
·        Animal FAS enzymes consist of (alpha)2 homodimers
·        Fungal FAS enzymes consist of (alpha)6(beta)6 dodecamers
·        A few bacterial FAS enzymes consist of (alpha)6 hexamers
           Type I FAS systems carry out multiple steps of fatty acid synthesis in each sterically isolated reaction chamber.  Mammalian FAS is thought to have evolved through gene fusion.

Type II FAS systems

In type II FAS systems, the enzymes exist as distinct, individual proteins, where each protein catalyses a single step in the reaction pathway.  Most prokaryotic FAS systems fall into this category, as well as certain plant FAS systems.


Fatty Acid Synthesis Proceeds in a Repeating Reaction Sequence

In all organisms, the long carbon chains of fatty acids are assembled in a repeating four-step sequence. A saturated acyl group produced by each four-step series of reactions becomes the substrate for subsequent condensation with an activated malonyl group. With each passage through the cycle, the fatty acyl chain is extended by two carbons. Both the electron-carrying cofactor and the activating groups in the reductive anabolic sequence differ from those in the oxidative catabolic process. Recall that in  oxidation, NAD and FAD serve as electron acceptors and the activating group is the thiol (—SH) group of coenzyme A. By contrast, the reducing agent in the synthetic sequence is NADPH and the activating groups are two different enzyme-bound —SH groups. There are two major variants of fatty acid synthase: fatty acid synthase I (FAS I), found in vertebrates and fungi, and fatty acid synthase II (FAS II), found in plants and bacteria. The FAS I found in vertebrates consists of a single multifunctional polypeptide chain. The mammalian FAS I is the prototype. Seven active sites for different reactions lie in separate domains. The mammalian polypeptide functions as a  homodimer. The subunits appear to function independently. When all the active sites in one subunit are inactivated by mutation, fatty acid synthesis is only modestly reduced. A somewhat different FAS I is found in yeast and other fungi, and is made up of two multifunctional polypeptides that form a complex with an architecture distinct from the vertebrate systems (Fig. 21–3b). Three of the seven required active sites are found on the  subunit and four on the subunit.



Addition of two carbons to a growing fatty acyl chain: a four-step sequence. Each malonyl group and acetyl (or longer acyl) group is activated by a thioester that links it to fatty acid synthase, a multienzyme system described later in the text.

1 Condensation of an activated acyl group (an acetyl group from acetyl-CoA is the first acyl group) and two carbons derived from malonyl-CoA, with elimination of CO2 from the malonyl group, extends the acyl chain by two carbons. The mechanism of the first step of this reaction is given to illustrate the role of decarboxylation in facilitating condensation. The -keto product of this condensation is then reduced in three more steps nearly identical to the reactions of  oxidation, but in the reverse sequence:

2 the -keto group is reduced to an alcohol

3 elimination of H2O creates a double bond, and

4 the double bond is reduced to form the corresponding saturated fatty acyl group.




The structure of fatty acid synthase type I systems. The low-resolution structures of (a) the mammalian and (b) fungal enzyme systems are shown. (a) All of the active sites in the mammalian system are located in different domains within a single large polypeptide chain. The different enzymatic activites are: 

-ketoacyl-ACP synthase (KS),
-malonyl/acetyl-CoA
–ACP transferase (MAT),
-hydroxyacyl-ACP dehydratase (DH),
-enoyl-ACP reductase (ER),
-ketoacyl-ACP reductase (KR).

ACP is the acyl carrier protein. The linear arrangement of the domains in the polypeptide is shown in the lower panel. The seventh domain (TE) is a thioesterase that releases the palmitate product from ACP when the synthesis is completed. The ACP and TE domains are disordered in the crystal and are therefore not shown in the structure. (b) In the structure of the FAS I from the fungus Thermomyces lanuginosus, the same active sites are divided between two multifunctional polypeptide chains that function together. Six copies of each polypeptide are found in the heterododecameric complex. A wheel of sixsubunits, which include ACP as well as the KS and KR active sites, is found at the center of the complex. In the wheel three subunits are found on one face, three on the other. On either side of the wheel are domes formed by trimers of the  subunits (containing the ER and DH active sites, as well as two domains with active sites analogous to MAT in the mammalian enzyme). The domains of one of each type of subunit are colored according to the active site colors of the mammalian enzyme in (a).





With FAS I systems, fatty acid synthesis leads to a single product, and no intermediates are released. When the chain length reaches 16 carbons, that product (palmitate, 16:0) leaves the cycle. Carbons C-16 and C-15 of the palmitate are derived from the methyl and carboxyl carbon atoms, respectively, of an acetyl-CoA used directly to prime the system
at the outset



The rest of the carbon atoms in the chain are derived from acetyl-CoA via malonyl-CoA. FAS II, in plants and bacteria, is a dissociated system; each step in the synthesis is catalyzed by a separate and freely diffusible enzyme. Intermediates are also diffusible and may be diverted into other pathways (such as lipoic acid synthesis). Unlike FAS I, FAS II generates a variety of products, including saturated fatty acids of several lengths, as well as unsaturated, branched, and hydroxy fatty acids. An FAS II system is also found in vertebrate mitochondria. The discussion to follow will focus on the mammalian FAS I.

The Mammalian Fatty Acid Synthase Has Multiple Active Sites

The multiple domains of mammalian FAS I function as distinct but linked enzymes. The active site for each enzyme is found in a separate domain within the larger polypeptide. Throughout the process of fatty acid synthesis, the intermediates remain covalently attached as  thioesters to one of two thiol groups. One point of attachment is the —SH group of a Cys residue in one of the synthase domains (-ketoacyl-ACP synthase; KS); the other is the —SH group of acyl carrier protein, a separate domain of the same polypeptide. Hydrolysis of thioesters is highly exergonic, and the energy released helps to make two different steps ( 1 and 5 in Fig. below) in fatty acid synthesis (condensation) thermodynamically favorable.

Acyl carrier protein (ACP) is the shuttle that holds the system together. The Escherichia coli ACP is a small protein  containing the prosthetic group 4-phosphopantetheine The 4-phosphopantetheine prosthetic group of E. coli ACP is believed to serve as a flexible arm, tethering the growing fatty acyl chain to the surface of the fatty acid synthase complex while carrying the reaction intermediates from one enzyme active site to the next. The ACP of mammals has a similar function and the same prosthetic group; as we have seen, however, it is embedded as a domain in a much larger multifunctional polypeptide.



Fatty Acid Synthase Receives the Acetyl and Malonyl Groups

Before the condensation reactions that build up the fatty acid chain can begin, the two thiol groups on the enzyme complex must be charged with the correct acyl groups: ( Figure below, top ) First, the acetyl group of acetyl-CoA is transferred to ACP in a reaction catalyzed by the malonyl /acetyl-CoA–ACP transferase (MAT in Fig. below) domain of the multifunctional polypeptide. The acetyl group is then transferred to the Cys —SH group of the -ketoacyl-ACP synthase (KS). The second reaction, transfer of the malonyl group from malonyl-CoA to the —SH group of ACP, is also catalyzed by malonyl/acetyl-CoA–ACP transferase. In the charged synthase complex, the acetyl and malonyl groups are activated for the chain-lengthening process. 


The first four steps of this process are now considered in some detail; all step numbers refer to figure above:

Step 1 Condensation The first reaction in the formation of a fatty acid chain is a formal Claisen condensation involving the activated acetyl and malonyl groups to form acetoacetyl-ACP, an acetoacetyl group bound to ACP through the phosphopantetheine —SH group; simultaneously, a molecule of CO2 is produced. In this reaction, catalyzed by -ketoacyl-ACP synthase, the acetyl group is transferred from the Cys —SH group of the enzyme to the malonyl group on the —SH of ACP, becoming the methyl-terminal two-carbon unit of the new acetoacetyl group. The carbon atom of the CO2 formed in this reaction is the same carbon originally introduced into malonyl- CoA from HCO3 by the acetyl-CoA carboxylase reaction. Thus CO2 is only transiently in covalent linkage during fatty acid biosynthesis; it is removed as each two-carbon unit is added. Why do cells go to the trouble of adding CO2 to make a malonyl group from an acetyl group, only to lose the CO2 during the formation of acetoacetate? Recall that in the  oxidation of fatty acids, cleavage of the bond between two acyl groups (cleavage of an acetyl unit from the acyl chain) is highly exergonic, so the simple condensation of two acyl groups (two acetyl-CoA molecules, for example) is highly endergonic. The use of activated malonyl groups rather than acetyl groups is what makes the condensation reactions thermodynamically favorable. The methylene carbon (C-2) of the malonyl group, sandwiched between carbonyl and carboxyl carbons, is chemically situated to act as a good nucleophile. In the condensation step (step 1 ), decarboxylation of the malonyl group facilitates the nucleophilic attack of the methylene carbon on the thioester linking the acetyl group to -ketoacyl-ACP synthase, displacing the enzyme’s —SH group. Coupling the condensation to the decarboxylation of the malonyl group renders the overall process highly exergonic. A similar carboxylation-decarboxylation sequence facilitates the formation of phosphoenolpyruvate from pyruvate in gluconeogenesis. By using activated malonyl groups in the synthesis of fatty acids and activated acetate in their degradation, the cell makes both processes energetically favorable, although one is effectively the reversal of the other. The extra energy required to make fatty acid synthesis favorable is provided by the ATP used to synthesize malonyl- CoA from acetyl-CoA and HCO3

Step 2 Reduction of the Carbonyl Group. The acetoacetyl-ACP formed in the condensation step now undergoes reduction of the carbonyl group at C-3 to form D--hydroxybutyryl-ACP. This reaction is catalyzed by-ketoacyl-ACP reductase (KR) and the electron donor is NADPH. Notice that the D--hydroxybutyryl group does not have the same stereoisomeric form as the L--hydroxyacyl intermediate in fatty acid oxidation.

Step 3 Dehydration The elements of water are now removed from C-2 and C-3 of D--hydroxybutyryl-ACP to yield a double bond in the product, trans-2- butenoyl-ACP. The enzyme that catalyzes this dehydration is -hydroxyacyl-ACP dehydratase (DH).

Step 4 Reduction of the Double Bond. Finally, the double bond of trans-2-butenoyl-ACP is reduced (saturated) to form butyryl-ACP by the action of enoyl-ACP reductase (ER); again, NADPH is the electron donor.

The Fatty Acid Synthase Reactions Are Repeated to Form Palmitate

Production of the four-carbon, saturated fatty acyl–ACP marks completion of one pass through the fatty acid synthase complex. The butyryl group is now transferred from the phosphopantetheine —SH group of ACP to the Cys —SH group of -ketoacyl-ACP synthase, which initially bore the acetyl group (Fig. above). To start the next cycle of four reactions that lengthens the chain by two more carbons, another malonyl group is linked to the now unoccupied phosphopantetheine —SH group of ACP



Condensation occurs as the butyryl group, acting like the acetyl group in the first cycle, is linked to two carbons of the malonyl-ACP group with concurrent loss of CO2. The product of this condensation is a six-carbon acyl group, covalently bound to the phosphopantetheine—SH group. Its -keto group is reduced in the next three steps of the synthase cycle to yield the saturated acyl group, exactly as in the first round of reactions—in this case forming the six-carbon product. Seven cycles of condensation and reduction produce the 16-carbon saturated palmitoyl group, still bound to ACP. For reasons not well understood, chain elongation by the synthase complex generally stops at this point and free palmitate is released from the ACP by a hydrolytic activity (thioesterase; TE) in the multifunctional protein.

We can consider the overall reaction for the synthesis of palmitate from acetyl-CoA in two parts. First, the formation of seven malonyl-CoA molecules: then seven cycles of condensation and reduction: Note that only six net water molecules are produced, because one is used to hydrolyze the thioester linking the palmitate product to the enzyme. The biosynthesis of fatty acids such as palmitate thus requires acetyl-CoA and the input of chemical energy in two forms: the group transfer potential of ATP and the reducing power of NADPH. The ATP is required to attach CO2 to acetyl-CoA to make malonyl-CoA; the NADPH is required to reduce the double bonds. In nonphotosynthetic eukaryotes there is an additional cost to fatty acid synthesis, because acetyl-CoA is generated in the mitochondria and must be transported to the cytosol. As we will see, this extra step consumes
two ATPs per molecule of acetyl-CoA transported, increasing the energetic cost of fatty acid synthesis to three ATPs per two-carbon unit.

Fatty Acid Synthesis Occurs in the Cytosol of Many Organisms but in the Chloroplasts of Plants

In most higher eukaryotes, the fatty acid synthase complex is found exclusively in the cytosol, as are the biosynthetic enzymes for nucleotides, amino acids, and glucose. This location segregates synthetic processes from degradative reactions, many of which take place in the mitochondrial matrix. There is a corresponding segregation of the electron-carrying cofactors used in anabolism (generally a reductive process) and those used in catabolism (generally oxidative).



Usually, NADPH is the electron carrier for anabolic reactions, and NAD serves in catabolic reactions. In hepatocytes, the [NADPH]/[NADP] ratio is very high (about 75) in the cytosol, furnishing a strongly reducing environment for the reductive synthesis of fatty acids and other biomolecules. The cytosolic [NADH]/[NAD] ratio is much smaller (only
about 8  104), so the NAD-dependent oxidative catabolism of glucose can take place in the same compartment, and at the same time, as fatty acid synthesis. The [NADH]/[NAD] ratio in the mitochondrion is much higher than in the cytosol, because of the flow of electrons to NAD from the oxidation of fatty acids, amino acids, pyruvate, and acetyl-CoA. This high mitochondrial [NADH]/[NAD] ratio favors the reduction of oxygen via the respiratory chain.

Acetate Is Shuttled out of Mitochondria as Citrate

In nonphotosynthetic eukaryotes, nearly all the acetyl- CoA used in fatty acid synthesis is formed in mitochondria from pyruvate oxidation and from the catabolism of the carbon skeletons of amino acids.

That means, fatty acid synthesis in eukaryotes is interdependent with mitochondria and carbon skeletons of amino acids. 

Acetyl-CoA arising from the oxidation of fatty acids is not a significant source of acetyl-CoA for fatty acid biosynthesis in animals, because the two pathways are reciprocally regulated. The mitochondrial inner membrane is impermeable to acetyl-CoA, so an indirect shuttle transfers acetyl group equivalents across the inner membrane


Intramitochondrial acetyl-CoA first reacts with oxaloacetate to form citrate, in the citric acid cycle reaction catalyzed by citrate synthase

That means the citric acid cycle must also be in place already

Citrate then passes through the inner membrane on the citrate transporter. In the cytosol citrate cleavage by citrate lyase regenerates acetyl-CoA and oxaloacetate in an ATP-dependent reaction. Oxaloacetate cannot return to the mitochondrial matrix directly, as there is no oxaloacetate transporter. Instead, cytosolic malate dehydrogenase reduces the oxaloacetate to malate, which can return to the mitochondrial matrix on the malate–-ketoglutarate transporter in exchange for citrate. In the matrix, malate is reoxidized to oxaloacetate to complete the shuttle. However, most of the malate produced in the cytosol is used to generate cytosolic NADPH through the activity of malic enzyme (Fig.a).



The pyruvate produced is transported to the mitochondria by the pyruvate transporter, and converted back into oxaloacetate by pyruvate carboxylase in the matrix. The resulting cycle results in the consumption of two ATPs (by citrate lyase and pyruvate carboxylase) for every molecule of acetyl-CoA delivered to fatty acid synthesis. After citrate cleavage to generate acetyl-CoA, conversion of the four remaining carbons to pyruvate and CO2 via malic enzyme generates about half the NADPH required for fatty acid synthesis. The pentose phosphate pathway contributes the rest of the needed NADPH.

Citrate Shuttle 6

• FAs are synthesized in the cytoplasm from acetylCoA
• AcetylCoA generated from pyruvate by the action of PDH
and by β-oxidation of fatty acids is in the mitochondria.
• For fatty acid biosynthesis, acetylCoA has to be transported
from the mitochondria to the cytoplasm. This is done via a
shuttle system called the Citrate Shuttle.
• AcetylCoA reacts with oxaloacetate to give citrate. A
tricarboxylate translocase transports citrate from
mitochondria to cytosol.
• In the cytosol, citrate is cleaved back to oxaloacetate and
acetylCoA. This reaction is catalyzed by ATP-citrate lyase
and requires the hydrolysis of one molecule of ATP.

Fatty Acid Biosynthesis Is Tightly Regulated

When a cell or organism has more than enough metabolic fuel to meet its energy needs, the excess is generally converted to fatty acids and stored as lipids such as triacylglycerols. The reaction catalyzed by acetyl-CoA carboxylase is the rate-limiting step in the biosynthesis of fatty acids, and this enzyme is an important site of regulation. In vertebrates, palmitoyl-CoA, the principal product of fatty acid synthesis, is a feedback inhibitor of the enzyme; citrate is an allosteric activator (Fig. a) increasing Vmax.



Citrate plays a central role in diverting cellular metabolism from the consumption (oxidation) of metabolic fuel to the storage of fuel as fatty acids. When the concentrations of mitochondrial acetyl-CoA and ATP increase, citrate is transported out of mitochondria; it then becomes both the precursor of cytosolic acetyl-CoA and an allosteric signal for the activation of acetyl-CoA carboxylase. At the same time, citrate inhibits the activity of phosphofructokinase-1, reducing the flow of carbon through glycolysis. Acetyl-CoA carboxylase is also regulated by covalent modification. Phosphorylation, triggered by the hormones glucagon and epinephrine, inactivates the enzyme and reduces its sensitivity to activation by citrate, thereby slowing fatty acid synthesis. In its active (dephosphorylated) form, acetyl-CoA carboxylase polymerizes into long filaments (Fig.b above); phosphorylation is accompanied by dissociation into monomeric subunits and loss of activity. The acetyl-CoA carboxylase of plants and bacteria is not regulated by citrate or by a phosphorylationdephosphorylation cycle. The plant enzyme is activated by an increase in stromal pH and [Mg2], which occurs on illumination of the plant. Bacteria do not use triacylglycerols as energy stores. In E. coli, the primary role of fatty acid synthesis is to provide precursors for membrane lipids; the regulation of this process is complex, involving guanine nucleotides (such as ppGpp) that coordinate cell growth with membrane formation. In addition to the moment-by-moment regulation of enzymatic activity, these pathways are regulated at the level of gene expression. For example, when animals ingest an excess of certain polyunsaturated fatty acids, the expression of genes encoding a wide range of lipogenic enzymes in the liver is suppressed. The detailed mechanism by which these genes are regulated is not yet clear.
If fatty acid synthesis and  oxidation were to proceed simultaneously, the two processes would constitute a futile cycle, wasting energy.  Oxidation is blocked by malonyl-CoA, which inhibits carnitine acyltransferase I. Thus during fatty acid synthesis, the production of the first intermediate, malonyl-CoA, shuts down  oxidation at the level of a transport system in the mitochondrial inner membrane. This control mechanism illustrates another advantage of segregating synthetic and degradative pathways in different cellular compartments.

1) https://en.wikipedia.org/wiki/Fatty_acid_synthesis
2) https://www.ebi.ac.uk/interpro/potm/2007_6/Page1.htm
3) https://en.wikipedia.org/wiki/Fatty_acid_metabolism
4) http://creation.com/origin-of-life
5) http://pubs.rsc.org/en/content/articlelanding/2014/mb/c4mb00443d/unauth#!divAbstract
6) http://www.csun.edu/~jm77307/Fatty%20Acid%20Biosynthesis.pdf

further readings :
http://www.godandscience.org/evolution/origin_membranes.html
http://www.bioinfo.org.cn/book/biochemistry/chapt20/sim1.htm
https://s10.lite.msu.edu/res/msu/botonl/b_online/e19/19i.htm
http://oregonstate.edu/dept/biochem/hhmi/hhmiclasses/biochem/lectnoteskga/2kjan19lecturenotes.html
http://www.sciencemag.org/content/311/5765/1263.figures-only
http://www.sciencemag.org/content/311/5765/1258.full
http://pt.slideshare.net/namarta28/fatty-acid-synthesis-13753491
http://www.yale.edu/xiong/publications/FAS-Cell07.pdf

The origin of life on Earth is a set of paradoxes. In order for life to have gotten started, there must have been a genetic molecule -- something like DNA or RNA -- capable of passing along blueprints for making proteins, the workhorse molecules of life. But modern cells can't copy DNA and RNA without the help of proteins themselves. To make matters more vexing, none of these molecules can do their jobs without fatty lipids, which provide the membranes that cells need to hold their contents inside. And in yet another chicken-and-egg complication, protein-based enzymes (encoded by genetic molecules) are needed to synthesize lipids. 1

Fatty Acid Synthesis: A Machine with “High Degree of Architectural Complexity” 4

As Bruce Alberts said in 1998, the biology of the future was going to be the study of molecular machines: “the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.”  One of those machines is like a mini-factory in itself.  It’s called


Fatty acid synthase (FAS)  

Three Yale researchers just published the most detailed description of this machine in the journal Cell. They remarked that its most striking feature is the “high degree of architectural complexity” – some 48 active sites, complete with moving parts, in a particle 27 billionths of a meter high and 23 billionths of a meter wide. Despite our aversion to fat, fatty acids are essential to life.  It’s when fat production goes awry that you can become fat.  The authors explain:


Fatty acids are key components of the cell, and their synthesis is essential for all organisms except archaea.  They are major constituents of cellular membranes and are used for posttranslational protein modifications that are functionally important.  Saturated fatty acids are the main stores of chemical energy in organisms.  Deregulation of fatty acid synthesis affects many cellular functions and may result inaberrant mitosis, cancer, and obesity.

The chemical steps for building fatty acids appear in the simplest cells and remain essentially unchanged up to the most complex organisms, although the machinery differs widely between plants, animals and bacteria.  In plants, for instance, the steps are performed by separate enzymes.  In animals, a two-part machine does the work.  Which organism has one of the most elaborate fatty-acid machines of all?  The surprising answer: fungi.  The researchers imaged the fatty acid synthase enzymes of yeast and, despite their academic restraint, were clearly excited as the details came into focus:


Perhaps the most striking feature of fungal FAS is its high degree of architectural complexity, in which 48 functional centers exist in a single ... particle.  Detailed structural information is essential for delineating how this complex particle coordinates the reactions involved in many steps of synthesis of fatty acids.... The six alpha subunits form a central wheel in the assembly, and the beta subunits form domes on the top and bottom of the wheel, creating six reaction chambers within which each ACP can reach the six active sites through surprisingly modest movements.  This structure now provides a complete framework for understanding the structural basis of this macromolecular machine’s important function.

Calling it an “elegant mechanism,” they proudly unveiled a new model that tells the secret inside: a swinging arm delivers parts to eight different reaction centers in a precise sequence.
     Some of the protein parts provide structural support for the delicate moving parts inside.  Taking the structure apart, it looks something like a wagon wheel with tetrahedron-shaped hubcaps above and below.  Picture a horizontal wagon wheel with three spokes, bisecting the equator of the structure.  Now put the hubcaps over the top and bottom axles.  The interior gets divided up into six compartments (“reaction chambers”) where the magic takes place.´



    In each reaction chamber, eight active sites are positioned on the walls at widely separated angles from the center.  Spaced nearly equidistant between them all is a pivot point, and attached to it by a hinge is a lever arm.  This lever arm, called ACP, is just the right length to reach all of the reaction sites.  From a tunnel on the exterior, the first component arrives and is fastened to the ACP arm (priming).  The arm then swings over to another active site to pick up the next part, then cycles through the next six reaction sites that each do their part to add ingredients to the growing fatty acid chain (elongation).  The machine cycles through the elongation step multiple times, adding carbons to the growing fatty acid.  When the chain reaches its proper length (16-18 carbons, depending on the fatty acid needed), it is sent to a final active site that stops the cycle (termination) and delivers the product through an exit channel to the cytoplasm.


The ACP hinged arm, then, is the key to the system.  Imagine a life-size automated factory with a roughly spherical interior.  Its task is to build a chain of parts in a precise order.  The first ingredient comes through a shaft and is attached to the robotic arm in the center.  The arm then follows a pre-programmed sequence that holds out the product to eight different machines on the walls that add their part to the product.  The final operation of the arm delivers the product to an exit channel.  In a cell, though, how does this arm actually move?  The answer: electricity.


Yes, folks, yeast cells contain actual electrical machines.  Don’t visualize wires of flowing current; instead, picture active sites with concentrations of positive and negative charges in precise amounts.  How does the lever arm use this electrical system?  Owing to the specific kinds of amino acids used, each active site has a net positive charge, while the ACP lever arm has a negative charge.  Each time a part is added to the product, it changes the overall charge distribution and makes the arm swing over to the next position.  Thus, a blind structure made out of amino acids follows a cyclic pattern that builds up a specific product molecule one carbon at a time, and automatically delivers it when complete.  After delivery, the system is automatically reset for the next round.  Clearly, the precision of charge on each active site is critical to the function of the machine.


Now that we have described one reaction chamber, step back and see that the yeast FAS machine has six such chambers working independently and simultaneously.  Another surprise is that the lever arm inside must be activated from the outside during assembly of the machine by a structure (PPT) on the exterior wall before it can work.  There’s a reason for this, too:

The crystal structure of yeast FAS reveals that this large, macromolecular assembly functions as a six-chambered reactor for fatty acid synthesis.  Each of the six chambers functions independently and has in its chamber wall all of the catalytic units required for fatty acid priming, elongation, and termination, while one substrate-shuttling component, ACP, is located inside each chamber and functions like a swinging arm.  Surprisingly, however, the step at which the reactor is activated must occur before the complete assembly of the particle since the PPT domain that attaches the pantetheine arm to ACP lies outside the assembly,inaccessible to ACP that lies inside.  Remarkably, the architectural complexity of the FAS particle results in the simplicity of the reaction mechanisms for fatty acid synthesis in fungi.

Maybe the activation step is a quality-control step, to ensure the system doesn’t cause trouble in the cytoplasm before the machinery is completely assembled. The authors did not mention how fast the synthesis takes place.  But if it’s anything like the other machinery in the cell, you can bet the FAS machine cranks out its products swiftly and efficiently, and life goes on, one molecule at a time.  Baking a cake with yeast will never seem the same again.


Reading this paper was almost a transcendent experience.  To imagine this level of precision and master-controlled processing on a level this small, cannot help but induce a profound sense of wonder and awe.  Here, all this time, this machine has been helping to keep living things functioning and we didn’t even know the details till now.  How would such revelations have affected the history of ideas?
    The authors did not say a peep about evolution except to note five times that certain parts are “conserved” (unevolved).  They also assumed evolution (without evidence) in one astonishing reaction to the fact that certain folds in the protein parts of this machine are unique in nature: listen – “They consequentially represent new folds and may have evolved independently to tether and orient the multiple active centers of fungal FAS for efficient catalysis.”  OK, everyone, a collective rotten-tomato toss for that enlightened suggestion.
    Remember that origin-of-life researchers are stumbling and fumbling trying to get even single amino acids to form, let alone get them to join up in useful, functioning chains.    The fatty acids are useless without the amino acids, and vice versa .  Even if some kind of metabolic cycle were to be envisioned under semi-realistic conditions, how did this elaborate machine, composed of amino acids with precise charge distributions, arise?  It’s not just the machine, it’s the blueprints and construction process that must be explained.  What blind process led to the precise placement of active sites that process their inputs in a programmed sequence?  What put them into a structure with shared walls where six reaction chambers can work independently?  All this complexity, involving thousands of precision amino acids in FAS (2.6 million atomic mass units) has to be coded in DNA, then built by the formidably complex translation process, then assembled together in the right order, or FAS won’t work.  But the storage, retrieval, translation and construction systems all need the fatty acids, too, or they won’t work.
    We are witnessing an interdependent system of mind-boggling complexity that defies any explanation besides intelligent design.  Yes, Bruce Alberts, “as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered.”  We have tended to “vastly underestimate the sophistication of many of these remarkable devices.”
    Yeast.  Who could have ever imagined this simple little blob possessed a high degree of architectural complexity and robotic technology.  Many questions remain.  Why do plants and animals have different mechanisms, but the same chemical steps?  Why do fungi, of all things, have the most elaborate architectures?  Are the other architectures equally complex in their own ways?  What other factories regulate this one, and how does this factory regulate other downstream systems?  We have much more to learn about fatty acid synthesis, but the “biology of the future” – design biology – is shedding far more light than Darwin’s myths ever did.  The fact that life functions so well, from yeast to human, should spur us on to uncover the design principles that make it all come together as a finely tuned system, in a finely tuned world, in a finely tuned universe. 


In Praise of Fat

Well, great balls of fat.  Cells have spherical globs of lipid (fat) molecules that never had gotten much attention nor respect.  They have been called lipid droplets, oil bodies, fat globules and other names suggesting they were just the beer bellies of the cell.  Not any more.  Scientists have been taking a closer look at these globs and are finding them to be dynamic, functional sites of critical metabolic activity.  No longer are they bags of superfluous undesirable molecules: they have been promoted to essential organelles, named adiposomes.
   Mary Beckman introduced two papers in Science with a summary of the new discoveries.


Whatever their name, these intracellular blobs of triglycerides or cholesterol esters, encased in a thin phospholipid membrane, are catching the attention of more and more biologists.  It turns out these lively balls of fathave as many potential roles within cells and tissues as they have names.  Pockmarked with proteins with wide-ranging biochemical activities, they shuffle components around the cell, store energy in the form of neutral lipids, and possibly maintain the many membranes of the cell.  The particles could also be involved in lipid diseases, diabetes, cardiovascular trouble, and liver problems. 



Beckman discussed several recent findings demonstrating what happens when fat regulation by adiposomes is disrupted.



 Since there is still much to be learned about adiposomes, Beckman mainly teased the readers with the possibilities that lie ahead.  She quoted one biologist who called the biology of lipid droplets “immense and untapped.”
   A Perspectives paper in the same issue by Stuart Smith introduced new findings about the machines that make fat.  He summarized a paper by Maier, Jenni and Ban revealing, in unprecedented detail, the structure of mammalian Fatty Acid Synthase (FAS), and another by the same authors plus Leibundgut about the comparable FAS machine in fungi. The former looks somewhat like a flying saucer; the latter, like a wheel with spokes from the top, or a complex cage from the side.  The diagrams of these machines point out “active sites” and “reaction chambers” where complex molecules are assembled in a specific sequence. The machines apparently have moving parts. The conclusion of the mammalian FAS paper hints how everything must be done in order and with the right specifications:


The overall architecture of mammalian FAS has been revealed by x-ray crystallography at intermediate resolution.  The dimeric [two-part] synthase adopts an asymmetric X-shaped conformation with two reaction chambers on each side formed by a full set of enzymatic domains required for fatty acid elongation, which are separated by considerable distances.  Substantial flexibility of the reaction chamber must accompany the handover of reaction intermediates during the FAS cycle, and further conformational transitions are required to explain the presence of alternative inter- and intrasubunit synthetic routes in FAS.  The results presented here provide a new structural basis to further experiments required for a detailed understanding of the complex mechanism of mammalian FAS.

Even for the fungal machine, the authors spoke of the “remarkable architectural principles” it exemplifies.

The closer they look, the more wondrous the cell gets.  Who would have thought that blobs of fat would contain machinery with moving parts and reaction chambers?  Who would have imagined their surfaces would be covered with complex proteins that regulate the production inside?  Who would have realized that fat was so important, the cell had complex assembly plants to build it?  Fat is almost a mild cussword in our vocabulary, but it is another class of molecular building blocks we couldn’t live without.  Fats, sugars, proteins and nucleic acids all work together in life, from humans to lowly fungi.  Each class of molecules has immense variety, each is essential, and each is manufactured to spec by precision machinery.  What a wonderful post-Darwinian world.



Distinct organization of two eukaryotic fatty acid synthases.
(Left) Fungal fatty acid synthase assumes a barrel-like shape. (Right) Mammalian (porcine) fatty acid synthase is an asymmetric Xshape . Side views are shown. In the fungal enzyme, acetyl transferase loads the acetyl primer substrate whereas the malonyl/palmitoyl transferase loads malonyl moieties and releases the palmitoyl-CoA product. The animal synthase loads both substrates via the malonyl-CoA-/Acetyl CoA-ACP transacylase and unloads free palmitic acids via a thioesterase. The acyl carrier protein of the fungal synthase is posttranslationally modified by phophopantetheinyl transferases that are likely localized as timers at the barrel apices.

Multienzyme Structures of Eukaryotic Fatty Acid Synthases 5

Fatty acid synthesis is a central cellular pathway providing components for membranes, energy storage compounds and messenger molecules. Fatty acid synthases of higher organisms are large multifunctional proteins where many individual enzymes are brought together and form a “molecular assembly line” to catalyze the production of fatty acids. Yeast fatty acid synthase is an α6β6 heterododecameric  barrel-shaped particle, in which the entire fatty acid synthesis is microcompartmentalized in two large reaction chambers. Mammalian fatty acid synthase is an X-shaped molecule with a full set of catalytic sites present in each of two semicircular reaction chambers on both sides of the molecule. The structures explain how reaction substrates are efficiently transferred between and delivered to individual catalytic sites by covalent attachment to flexible acyl carrier protein domains.



Fatty Acid Synthesis 3

Synthesis of fatty acids is a central cellular process that has been studied for many decades. Fatty acids are used in the cell as energy storage compounds and as messenger molecules. Previously, individual steps of this process have been studied on isolated bacterial enzymes. However, in higher organisms, fatty acid synthesis is catalyzed by large multifunctional proteins where many individual enzymes are brought together to form a “molecular assembly line”. Our recent work focused on studying the architecture of two representative classes of fatty acid synthases in higher organisms. The fungal and mammalian systems reveal two different architectural solutions that allow these giant multi-enzymes to hand over the products of one enzymatic active site to the next.

As a culmination of many years of research in our group we have determined the high resolution structure of the fungal FAS particle. The atomic structure reveals that the flexible acyl carrier domain (ACP) is double anchored at opposite sides of the reaction chamber with implications on its range of motion. Furthermore, we have been able to visualize this flexible domain stalled at the synthetic stage of the reaction cycle. These results allow us to propose a plausible mechanistic model for substrate channeling, which involves circular precession of the ACP domain coupled with substrate delivery by a switchblade-like motion of the prosthetic group.
Mammalian fatty acid synthase (FAS) is a remarkably complex enzyme that carries seven functional domains on a single polypeptide chain of approximately 2500 amino acids and forms a 540,000 Da α_2 dimer. The essential FAS has a central role in the primary metabolism of mammalian cells.









1) http://www.evolutionnews.org/2015/03/solution_to_an_094611.html
2) http://www.mn.uio.no/ibv/forskning/grupper/protstruc/arrangementer/abstract_simon_jenni.pdf
3) https://www.mol.biol.ethz.ch/groups/ban_group/FAS
4) http://creationsafaris.com/crev200704.htm
5) http://www.mn.uio.no/ibv/forskning/grupper/protstruc/arrangementer/abstract_simon_jenni.pdf

Direct structural insight into the substrate-shuttling mechanism of yeast fatty acid synthase1

Yeast fatty acid synthase (FAS)  barrel-shaped multienzyme complex, which carries out cyclic synthesis of fatty acids.The multiple, partially occupied positions of the ACP within the reaction chamber provide direct structural insight into the substrate-shuttling mechanism of fatty acid synthesis in this large cellular machine.
Fatty acid synthase (FAS) is the key enzyme for the biosynthesis of fatty acids in living organisms.  Although fungal and mammalian FAS have very different structures, they conserve all the necessary enzymes found in the FAS type II systems required for fatty acid synthesis. Mammalian FAS  was found to be a highly flexible complex. The mobile acyl carrier protein (ACP) domain has not yet been directly observed in the mammalian FAS system.
The six α-subunits form an equatorial wheel, which divides the barrel into two separate domes, each consisting of three β-subunits. The α- and β-subunits define three reaction chambers per dome and contain eight catalytic centers. Of these, the α-subunit contributes the phosphopantetheinyl transferase (PPT), ACP, ketoacyl synthase (KS), ketoacyl reductase (KR), and part of the malonyl-palmitoyl transferase (MPT) domain. The β-subunit contributes the acetyl-transferase (AT), enoyl reductase (ER), dehydratase (DH), and the major part of the MPT domain (Fig. A).



The structure of yeast FAS (A). Domain organization of the FAS α (Left) and β (Right) polypeptides with the domains colored according to the scheme shown above. (B–G) 3D map of yeast FAS , without and with the domains of the x-ray structure  fitted as rigid bodies. The domains are colored according to the scheme shown in A.
(B, C) Side view of the α6β6-assembly.
(D, E) Central map section showing the α6-wheel.
(F, G) The helix pair near the KS dimer on the outside of the α6-wheel showing the helix pitch.

In the fungal FAS, the ACP is tethered by two flexible linkers, which connect it to the MPT domain and the central hub of the equatorial wheel. The linker domains define the radius of action of the ACP, which agrees broadly with the dimensions of the reaction chamber. With the exception of the PPT domain, the active sites of all catalytic domains face the reaction chambers in the interior of the FAS barrel. In addition to the catalytic domains, almost half of the yeast FAS molecular mass is contributed by six structural domains, two in the α-subunit (SD1-2α) and four in the β-subunit (SD1-4β). Previous studies  have shown that the reaction chambers work independently of one another.

Yeast, which mostly depends on endogenous fatty acid synthesis, has developed a rigid cage-like FAS machinery with six reaction chambers for the increased efficiency of fatty acid synthesis. Here, ACP is proposed to be the only mobile domain performing the substrate shuttling, unlike the open mammalian FAS structure with two reaction chambers where the efficiency of the fatty acid synthesis is determined by the high conformational flexibility of the complex.

The ACP belongs to a class of universal and highly conserved carrier proteins that bind acyl intermediates via the  phosphopantetheine arm and are active in various metabolic pathways, including the biosynthesis of polyketides or fatty acids.

In the multifunctional fungal fatty acid synthase (FAS), the acyl carrier protein (ACP) domain shuttles reaction intermediates covalently attached to its prosthetic phosphopantetheine group between the different enzymatic centers of the reaction cycle.




1) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889056/

Structural Basis for Substrate Delivery by Acyl Carrier Protein in the Yeast Fatty Acid Synthase 2 1

In the multifunctional fungal fatty acid synthase (FAS), the acyl carrier protein (ACP) domain shuttles reaction intermediates covalently attached to its prosthetic phosphopantetheine group between the different enzymatic centers of the reaction cycle. Here, we report the structure of the Saccharomyces cerevisiae FAS determined at 3.1 angstrom resolution with its ACP stalled at the active site of ketoacyl synthase. The ACP contacts the base of the reaction chamber through conserved, charge-complementary surfaces, which optimally position the ACP toward the catalytic cleft of ketoacyl synthase. The conformation of the prosthetic group suggests a switchblade mechanism for acyl chain delivery to the active site of the enzyme.

Acyl carrier protein (ACP) and related substrate shuttling domains are essential in many metabolic pathways, including fatty acid, polyketide, and nonribosomal protein biosynthesis. During fatty acid synthesis, substrates are linked via a thioester bond to the prosthetic phosphopantetheine (PPT) group of ACP. In the dissociated type II fatty acid synthase (FAS) systems of most bacteria and plants, ACP is a highly abundant, small protein, which sequentially transfers the acyl-chain intermediates between the different enzymes during the cyclic reaction. The type I FAS systems of mammals, fungi, and some bacteria comprise large, multifunctional enzymes into which ACP is integrated together with the catalytic domains. This leads to a drastically increased local concentration of ACP and of all catalytic domains and allows efficient catalysis by shuttling the reaction intermediates from one reaction center to the next.

Previous structural studies of bacterial and plant type II ACPs and related carrier domains revealed that the proteins fold into a flexible all α-helical bundle. A hydrophobic cavity formed within the helix bundle of ACP shows high structural plasticity, allowing it to accommodate thioester-bound acyl-chains of different lengths.Limited structural information about the interactions of ACP with catalytic enzymes and the mechanism of substrate delivery is currently available.



Three ACPs are stalled in each of the two reaction chambers in the heterododecameric yeast FAS complex.
(A) The superposition of the yeast (green) with the T. lanuginosus (light blue) FAS structure reveals a very high homology . Although ACP is disordered in the T. lanuginosus crystals, it is visible in yeast (red). One type of four-helix bundle at the periphery of the central wheel could only be built in T. lanuginosus FAS (indicated by an asterisk).
(B) Anchoring of ACP within the reaction chambers. The ACP domains, shown as red surfaces, are located between peripheral and central anchors, which are displayed as green ribbons. The flexible linkers L1 and L2, which double-tether ACP, are not seen in the electron density map but are schematically shown as dashed yellow lines. The refined portion of the PPT prosthetic group of ACP is shown in black.



Structure of yeast ACP bound to the KS catalytic cleft.
(A) The prosthetic PPT group (spheres) covalently attached to the ACP core (cyan) adopts an extended conformation in the fungal FAS complex. The ACP core forms a compact domain with an additional four-helix bundle (gray), rendering fungal ACP considerably larger than the bacterial counterpart (blue, shown in the same orientation). During interdomain substrate shuttling, the PTT arm might fold back on ACP (arrow), thereby inserting the acyl chain into a cavity formed by the ACP core, as observed in the isolated E. coli ACP structure.
(B) Detailed view of PPT bound in the catalytic cleft of KS. The unbiased threefold averaged Fobs – Fcalc simulated annealing omit map (green) shows ACP and the phosphate and pantoic acid (PA) moieties of the PPT prosthetic group. Modeling of the additional PPT part shows that the catalytic residues of KS can easily be reached. KS1 and KS2 form the dimer to which ACP is bound.



Mode of ACP binding to the central wheel and the catalytic cleft entrance of KS (gray)
(A) The extended prosthetic PPT group (magenta) of ACP (cyan) reaches into the catalytic pocket of KS (asterisk). Distal to the PPT arm, ACP is flexibly tethered to the central hub (green dot) and the peripheral anchor (dashed circle) at the interior of the dome (brown).
(B) Top and bottom views of ACP bound to the entrance cleft of KS via its core part and contacting the central wheel with the additional part.
(C) ACP binding is mediated by complementarily charged patches, as visualized by the electrostatic surface potential of the contact areas (blue, positive; red, negative).

Trapping the dynamic acyl carrier protein in fatty acid biosynthesis 2

Acyl carrier protein (ACP) transports the growing fatty acid chain between enzymatic domains of fatty acid synthase (FAS) during biosynthesis1. Because FAS enzymes operate on ACP-bound acyl groups, ACP must stabilize and transport the growing lipid chain. ACPs have a central role in transporting starting materials and intermediates throughout the fatty acid biosynthetic pathway. The transient nature of ACP–enzyme interactions impose major obstacles to obtaining high-resolution structural information about fatty acid biosynthesis, and a new strategy is required to study protein–protein interactions effectively. Here we describe the application of a mechanism-based probe that allows active site-selective covalent crosslinking of AcpP to FabA, the Escherichia coli ACP and fatty acid 3-hydroxyacyl-ACP dehydratase, respectively. We report the 1.9 Å crystal structure of the crosslinked AcpP–FabA complex as a homodimer in which AcpP exhibits two different conformations, representing probable snapshots of ACP in action: the 4′-phosphopantetheine group of AcpP first binds an arginine-rich groove of FabA, then an AcpP helical conformational change locks AcpP and FabA in place. Residues at the interface of AcpP and FabA are identified and validated by solution nuclear magnetic resonance techniques, including chemical shift perturbations and residual dipolar coupling measurements. These not only support our interpretation of the crystal structures but also provide an animated view of ACP in action during fatty acid dehydration. These techniques, in combination with molecular dynamics simulations, show for the first time that FabA extrudes the sequestered acyl chain from the ACP binding pocket before dehydration by repositioning helix III. Extensive sequence conservation among carrier proteins suggests that the mechanistic insights gleaned from our studies may be broadly applicable to fatty acid, polyketide and non-ribosomal biosynthesis. Here the foundation is laid for defining the dynamic action of carrier-protein activity in primary and secondary metabolism, providing insight into pathways that can have major roles in the treatment of cancer, obesity and infectious disease.



a, AcpP is a small, acidic protein comprised of four α-helices that interacts with at least 19 catalytic enzymes, 12 of which belong to FAS (10 shown here). The apolar interior of helix II (α2) and helix III (α3) form a hydrophobic cavity that sequesters the growing metabolite attached to the PPant arm. b, (top) A native substrate of FabA and (middle) modified AcpP with targeted sulfonyl-3-alkynyl crosslinking probe, derived from (bottom) the crosslinking pantetheinamide analog 1. c, Proposed mechanism of FabA. Protein-protein interactions between AcpP and FabA induce release of the sequestered substrate from AcpP into the active site of FabA, where dehydration is catalyzed. d, Crosslinking strategy to form AcpP=FabA with mechanism-based crosslinking probe 1.



a, X-ray crystal structure of AcpP=FabA at 1.9 Å. b, The molecular surface mapped with calculated vacuum electrostatic potential of AcpP=FabA. Blue shading indicates electro-positive and red shading indicates electro-negative protein surfaces. c, Rotating b 90° at the interfaces between each AcpP=FabA to visualize electrostatic pairing. d, Expanded view of both interfaces in AcpP=FabA, indicating salt bridges and hydrophobic interactions between helix II (α2) and helix III (α3) of AcpP and the Positive Patch of FabA. e, Comparison between hydrophobic cleft of AcpP with (top) sequestered substrate (from PDB: 2FAE, with long interior hydrophobic cavity outlined with dashed line) and (bottom) AcpP1 in AcpP=FabA (reduced interior cavity). f, The interior cavity of 2FAE labeled with the hydrophobic residues. The contraction of these hydrophobic residues collapses the interior cavity in AcpP=FabA.


1) http://www.sciencemag.org/content/316/5822/288.figures-only
2) http://www.ncbi.nlm.nih.gov/pubmed/24362570

How Are Fatty Acids Synthesized? 1

Formation of Malonyl-CoA Activates Acetate Units for Fatty Acid Synthesis

The design strategy for fatty acid synthesis is this:

1. Fatty acid chains are constructed by the addition of two-carbon units derived from acetyl -CoA.
2. The acetate units are activated by formation of malonyl-CoA (at the expense of ATP).
3. The addition of two-carbon units to the growing chain is driven by decarboxylation of malonyl-CoA.
4. The elongation reactions are repeated until the growing chain reaches 16 carbons in length (palmitic acid).
5. Other enzymes then add double bonds and additional carbon units to the chain.

Fatty Acid Biosynthesis Depends on the Reductive Power of NADPH

Levels of free fatty acids are very low in the typical cell. The palmitate made in this process is rapidly converted to CoA esters in preparation for the formation of triacylglycerols
and phospholipids

Cells Must Provide Cytosolic Acetyl-CoA and Reducing Power for Fatty Acid Synthesis

Eukaryotic cells face a dilemma in providing suitable amounts of substrate for fatty acid synthesis. Sufficient quantities of acetyl-CoA, malonyl-CoA, and NADPH must be generated in the cytosol for fatty acid synthesis. Malonyl-CoA is made by carboxylation of acetyl-CoA, so the problem reduces to generating sufficient acetyl-CoA and NADPH. There are three principal sources of acetyl-CoA (Figure below):

1. Amino acid degradation produces cytosolic acetyl-CoA.
2. Fatty acid oxidation produces mitochondrial acetyl-CoA.
3. Glycolysis yields cytosolic pyruvate, which (after transport into the mitochondria)
is converted to acetyl-CoA by pyruvate dehydrogenase.



The acetyl-CoA derived from amino acid degradation is normally insufficient for fatty acid biosynthesis, and the acetyl-CoA produced by pyruvate dehydrogenase and by fatty acid oxidation cannot cross the mitochondrial membrane to participate directly in fatty acid synthesis. Instead, acetyl-CoA is linked with oxaloacetate to form citrate, which is transported from the mitochondrial matrix to the cytosol (Figure above). 

The citrate carrier (CiC), a nuclear-encoded protein located in the mitochondrial inner membrane, is a member of the mitochondrial carrier family. CiC plays an important role in hepatic lipogenesis, which is responsible for the efflux of acetyl-CoA from the mitochondria to the cytosol in the form of citrate, the primer for fatty acid and cholesterol synthesis.2


Here it can be converted back into acetyl-CoA and oxaloacetate by ATP–citrate lyase. In this manner, mitochondrial acetyl-CoA becomes the substrate for cytosolic fatty acid synthesis. (Oxaloacetate returns to the mitochondria in the form of either pyruvate or malate, which is then reconverted to acetyl-CoA and oxaloacetate, respectively.) NADPH can be produced in the pentose phosphate pathway as well as by malic enzyme (Figure above). Reducing equivalents (electrons) derived from glycolysis in the form of NADH can be transformed into NADPH by the combined action of malate dehydrogenase and malic enzyme. Every malate oxidized by malic enzyme produces one NADPH, at the expense of a decarboxylation to pyruvate. Thus, when malate is oxidized, one NADPH is produced
for every acetyl-CoA. Conversion of 8 acetyl-CoA units to one palmitate would then be accompanied by production of 8 NADPH. (The other 6 NADPH required, would be provided by the pentose phosphate pathway.) On the other hand, for every malate returned to the mitochondria, one NADPH fewer is produced.

Acetate Units Are Committed to Fatty Acid Synthesis by Formation of Malonyl-CoA

Acetate units are the building blocks of fatty acids.  bicarbonate is required for fatty acid biosynthesis, this pathway involves synthesis of malonyl-CoA. The carboxylation of acetyl-CoA to form malonyl-CoA is essentially irreversible and is the committed step in the synthesis of fatty acids. The reaction is catalyzed by acetyl-CoA carboxylase, which
contains a biotin prosthetic group. This carboxylase is the only enzyme of fatty acid synthesis in animals that is not part of the multienzyme complex called fatty acid synthase.

http://www.dnatube.com/video/641/Fatty-Acid-Biosynthesis

The biosynthesis of saturated fatty acids requires a primer molecule, usually acetic acid in the form of its Coenzyme A ester, and a chain extender, malonyl-CoA. The latter is formed from acetyl CoA by the activity of the enzyme acetyl-CoA carboxylase in which biotin is the prosthetic group (and thus can be inhibited by avidin). In the first step of the reaction, carbon dioxide is linked to the biotin moiety, and this is subsequently transferred to acetyl-CoA to form malonyl-CoA. In microorganisms such as Escherichia coli, the enzyme complex comprises three dissociable proteins, but in plants and animals, the enzyme is a single multifunctional complex that exists in two main isoforms. Malonyl-CoA is also involved in the regulation of fatty acid oxidation by inhibiting carnitine palmitoyl-CoA transferase-1.

Acetyl-CoA Carboxylase Is Biotin-Dependent and Displays Ping-Pong Kinetics

The biotin prosthetic group of acetyl-CoA carboxylase is covalently linked to the E-amino group of an active-site lysine in a manner similar to pyruvate carboxylase. The reaction mechanism is also analogous to that of pyruvate carboxylase. ATP-driven carboxylation of biotin is followed by transfer of the activated CO2 to acetyl-CoA to form malonyl-CoA.

The enzyme from Escherichia coli has three subunits:

(1) a biotin carboxyl carrier protein (a dimer of 22.5-kD subunits);
(2) biotin carboxylase (a dimer of 51-kD subunits), which adds CO2 to the prosthetic group; and
(3) carboxyltransferase (an 22 tetramer with 30- and 35-kD subunits), which transfers the activated CO2 unit to acetyl-CoA.

The long, flexible biotin–lysine chain (biocytin) enables the activated carboxyl group to be carried between the biotin carboxylase and the carboxyltransferase



Acetyl-CoA Carboxylase in Animals Is a Multifunctional Protein

In animals, acetyl-CoA carboxylase (ACC) is a filamentous polymer. Each of the subunits contains the biotin carboxyl carrier moiety, biotin carboxylase, and carboxyltransferase activities, as well as allosteric regulatory sites. Animal ACC is thus a multifunctional protein. The polymeric form is active, but the  protomers are inactive.  Because this enzyme catalyzes the committed step in fatty acid biosynthesis, it is carefully regulated. Palmitoyl-CoA, the final product of fatty acid biosynthesis, shifts the equilibrium toward the inactive protomers, whereas citrate, an important allosteric activator of this enzyme, shifts the equilibrium toward the active polymeric form of the enzyme. Acetyl-CoA carboxylase shows the kinetic behavior of a Monod–Wyman– Changeux V-system allosteric enzyme in which allosteric effectors shift the T/R equilibrium between active R conformers and inactive T conformers.

Acyl Carrier Proteins Carry the Intermediates in Fatty Acid Synthesis

The basic building blocks of fatty acid synthesis are acetyl and malonyl groups, but they are not transferred directly from CoA to the growing fatty acid chain. Rather, they are first passed to ACP. This protein consists (in E. coli) of a single polypeptide chain of 77 residues to which is attached (on a serine residue) a phosphopantetheine group, the same group that forms the “business end” of coenzyme A. Thus, ACP is a somewhat larger version of coenzyme A, specialized for use in fatty acid biosynthesis.

Eukaryotes Build Fatty Acids on Megasynthase Complexes

The multiple enzyme domains of eukaryotic fatty acyl synthases are arrayed on large protein structures termed megasynthases. The individual enzyme domains of these structures in all eukaryotes are homologous to the corresponding small, discrete enzymes of bacterial FAS pathways. Remarkably, however, lower eukaryotes such as fungi and higher eukaryotes such as mammals have  entirely different megasynthase architectures for fatty acid synthesis. Mammalian homodimeric FAS has a flattened X-shape, whereas the fungal dodecameric FAS is a large, closed barrel, with two reaction chambers separated by equatorial stabilizing struts (Figure below).



In the fungal structure, the six -subunits form a central ring that is a “trimer of dimers” (Figure a,b)



Each -subunit contributes an extended -helical segment to the center of the structure. Pairs of these helices form three coiled-coil struts anchored by a six-helix bundle in the center of the barrel. Each alpha-subunit contains KR and KS domains. Three KR and three KS active sites are oriented toward the upper reaction chamber, and three of each face the lower chamber. The B-subunit trimers form rounded caps over the upper and lower reaction chambers. Each chamber contains three pores that allow substrates (acetyl-CoA and malonyl- CoA) to diffuse in and palmitoyl-CoA to exit. On each end of the structure, the active sites of the four beta-subunit enzyme domains  are oriented toward the interior of the reaction chamber. Three ACP domains in each chamber shuttle growing acyl chains from site to site during the catalytic cycle. Each ACP is tethered by two flexible linker peptides, which facilitate its site-to-site movement (Figure c above). The phosphopantetheine arm on each ACP can extend outward to reach into active sites or may retract to insert its acyl chain in a protective hydrophobic cavity during intersite transport. The homodimeric mammalian FAS contains all six functional enzyme domains on each subunit . In the X-shaped dimer, three of the domains—including KS, ER, and DH—form dimeric structures, whereas the KR and MAT domains are separated and lie near the ends of the extended “arms.” The arms form reaction chambers on either side of the structure. The flexible ACP domains do not appear in this structure (probably because they are not fixed in any one position in the crystals used for the structural studies). However, since it follows the KR domain in the polypeptide sequence, the ACP domain probably lies at the
end of each KR arm, where it can rotate to interact with the adjacent active sites. In both the fungal and the mammalian FAS structures, the close association of enzymic domains within one large complex permits efficient transfer of intermediates from one active site to the next. In addition, the presence of all these enzyme domains on one or two polypeptides allows the cell to coordinate synthesis of all enzymes needed for fatty acid synthesis.



C16 Fatty Acids May Undergo Elongation and Unsaturation

Additional Elongation  palmitate is the primary product of the fatty acid synthase. Cells synthesize many other fatty acids. Shorter chains are easily made if the chain is released before reaching 16 carbons in length. Longer chains are made through special elongation reactions, which occur both in the mitochondria and at the surface of the endoplasmic reticulum (ER). The ER reactions are actually quite similar to those we have just discussed: addition of twocarbon units at the carboxyl end of the chain by means of oxidative decarboxylations involving malonyl-CoA. As was the case for the fatty acid synthase, this decarboxylation provides the thermodynamic driving force for the condensation
reaction. The mitochondrial reactions involve addition (and subsequent reduction) of acetyl units. These reactions  are essentially a reversal of fatty acid oxidation, with the exception that NADPH is utilized in the saturation of the double bond, instead of FADH2.

Regulatory Control of Fatty Acid Metabolism Is an Interplay of Allosteric Modifiers and Phosphorylation–Dephosphorylation Cycles

The control and regulation of fatty acid synthesis is intimately related to regulation of fatty acid breakdown, glycolysis, and the TCA cycle. Acetyl-CoA is an important intermediate metabolite in all these processes. In these terms, it is easy to appreciate the interlocking relationships in the Figure below.



Malonyl-CoA can act to prevent fatty acyl-CoA derivatives from entering the mitochondria by inhibiting the carnitine acyltransferase of the outer mitochondrial membrane that initiates this transport. In this way, when fatty acid synthesis is turned on (as signaled by higher levels of malonyl-CoA), -oxidation is inhibited. As we pointed out earlier, citrate is an important allosteric activator of acetyl-CoA carboxylase, and fatty acyl-CoAs are inhibitors. The degree of inhibition is proportional to the chain length of the fatty acyl-CoA; longer chains show a higher affinity for the allosteric inhibition site on acetyl-CoA carboxylase. Palmitoyl-CoA, stearoyl-CoA, and arachidyl-CoA are the most potent inhibitors of the carboxylase.

Hormonal Signals Regulate ACC and Fatty Acid Biosynthesis

As described earlier, citrate activation and palmitoyl-CoA inhibition of acetyl-CoA carboxylase are strongly dependent on the phosphorylation state of the enzyme. This provides a crucial connection to hormonal regulation. Many of the enzymes that act to phosphorylate acetyl-CoA carboxylase  are controlled by hormonal signals. Glucagon is a good example



Glucagon binding to membrane receptors activates an intracellular cascade involving activation of adenylyl cyclase. Cyclic AMP produced by the cyclase activates a protein kinase, which then phosphorylates acetyl-CoA carboxylase. Unless citrate levels are high, phosphorylation causes inhibition of fatty acid biosynthesis. The carboxylase (and fatty acid synthesis) can be reactivated by a specific phosphatase, which dephosphorylates the carboxylase. Also indicated in the Figure above is the simultaneous activation by glucagon of triacylglycerol lipases, which hydrolyze triacylglycerols, releasing fatty acids for beta-oxidation. Both the inactivation of acetyl- CoA carboxylase and the activation of triacylglycerol lipase are counteracted by insulin, whose receptor acts to stimulate a phosphodiesterase that converts cAMP to AMP.


1) (4th ed.) (Reginald H. Garrett, Charles M. Grisham, 2010)

Assembly of MDa-sized FAS oligomeric structures 1

Johansson, Patrik; Mulinacci, Barbara; Koestler, Caecilia; Vollrath, Ronnald; Oesterhelt, Dieter; Grininger, Martin. (2009) Multimeric options for the auto-activation of the Saccharomyces cerevisiae FAS type I megasynthase. Structure, 17, 1063–1077.

S. cerevisiae FAS I is well studied; however, the assembly pathway of the heterododecamer is essentially unknown. Recent X-ray crystallographic studies revealed a functional conundrum. The ACP domain has to be post-translationally modified by a phosphopantetheine transferase (PPT) domain to drive fatty acid synthesis. However, in the fatty acid synthesis competent α6β6 FAS particle, domains are spatially separated so that post-translational modification cannot occur. Consequently, for full catalytic activity, the assembly of S. cerevisae FAS I from its subunits has to include a defined intermediate state where ACP and PPT can interact. Recently, we were able to show that PPT has to oligomerize to be catalytically competent, and that PPT is active as dimer and trimer, which constraints the possible conformations of a pre-complex (publ. 9).



Figure. ACP-PPT interaction within a α6β6 FAS particle. Besides the spatial separation of ACP and PPT in fungal FAS, the PPT and ACP cannot interact owing to spatial restraints. This figure shows the separation of ACP (magenta) and PPT (cyan). For clarity, a (physiologically non-relevant) α6 wheel substructure is shown. A sphere with a probe radius of 18 Å was used for surface calculation.Figure. Structure and domain organization of the fungal FAS.

Further information:
Under the assumption of conserved assembly pathways among several types of fungal FAS I, the interaction of β- and the α-chain might be an early event in fungal FAS I assembly. Considering an early interaction of chains and comforting the dimeric character of the domains KS and KR as well as of scaffolding elements, a pre-complex could have a α2β2 nature (publ. 17).

1) http://mg46.div.uni-frankfurt.de/research/fas

THE LIPID WORLD 1

Abstract. The continuity of abiotically formed bilayer membranes with similar structures in contemporary cellular life, and the requirement for microenvironments in which large and small molecules could be compartmentalized, support the idea that amphiphilic boundary structures contributed to the emergence of life.As an extension of this notion, we propose here a ‘Lipid World’ scenario as an early evolutionary step in the emergence of cellular life on Earth. This concept combines the potential chemical activities of lipids and other amphiphiles, with their capacity to undergo spontaneous self-organization into supramolecular structures such as micelles and bilayers. . In particular, the documented
chemical rate enhancements within lipid assemblies suggest that energy-dependent synthetic reactions could lead to the growth and increased abundance of certain amphiphilic assemblies.

In particular, it has been suggested that lipid membranes may have a hereditary potential, as most membranes are generated from other membranes but not created de novo. we propose an alternative view in which an original, highprobability ‘Lipid World’ later gave rise to a world populated by the complex, relatively improbable biopolymers that are ubiquitous in all life today. Among the large number of molecular species expected to be found on prebiotic Earth, lipid-like molecules have a distinct property: an ability to undergo spontaneous aggregation to form droplets, micelles, bilayers and vesicles within an aqueous phase, through entropy-driven hydrophobic interactions. While it is reasonable to assume that the first cellular life forms used amphiphilic molecules for boundary membranes, as well as for other functions, the origin and diversity of amphiphiles on the early Earth remains to be elucidated.

Self-assembly of amphiphilic molecules into complex supramolecular structures is spontaneous. The plausibility that such structures were present in the prebiotic environment is supported by the occurrence of amphiphilic molecules in carbonaceous meteorites and the demonstration that they can assemble into membrane vesicles.

This paper shows the helplessness of proponents of  natural prebiotic origin of lipids. Its a hudge gap between above explanation, and the arise of hypercomplex multyenzymatic protein complexes, which produce fatty acids through hyper complex multistep factory assembly-line like procedures.

1) http://ramet.elte.hu/~ramet/oktatas/IntegrativBiol/Segre_2001_OrigLifeEvolBiosph.pdf

The amazing fatty acid synthase nano-factories, and origin of life scenarios

https://reasonandscience.catsboard.com/t2168-the-amazing-fatty-acid-synthase-nano-factories-and-origin-of-life-scenarios#3950

The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.  Here we will give a closer look at fatty acids,  constituents of lipids, and their biosynthesis.

Lipids (‘fats’) are essential for the formation of a cell membrane that contains the cell contents, as well as for other cell functions. The cell membrane, comprised of several different complex lipids, is an essential part of a free-living cell that can reproduce itself.

Lipids have much higher energy density than sugars or amino acids, so their formation in any chemical soup is a problem for origin of life scenarios (high energy compounds are thermodynamically much less likely to form than lower energy compounds).  Fatty acids are hydrocarbon chains of various lengths. The ability to synthesize a variety of lipids is essential to all organisms.  Fatty acid synthesis requires the oxidation of the co-factor NADPH.

The major source of NADPH in animals and other non-photosynthetic organisms is the pentose phosphate pathway. Due to the complexity of the metabolic pathways, it has been argued that metabolism‐like chemical reaction sequences are unlikely to be catalysed by simple environmental catalysts.


This constitutes a serious problem for naturalistic explanations of the origin of life. The pentose phosphate pathway requires 7 enzymes, and is interdependent with glycolysis , since the beginning molecule for the pentose phosphate pathway is glucose-6-P, which is the second intermediate metabolite in glycolysis. 

Eukaryotic cells face a dilemma in providing suitable amounts of substrate for fatty acid synthesis. Sufficient quantities of acetyl-CoA, malonyl-CoA, and NADPH must be generated in the cytosol for fatty acid synthesis. Malonyl-CoA is made by carboxylation of acetyl-CoA, so the problem reduces to generating sufficient acetyl-CoA and NADPH. There are three principal sources of acetyl-CoA. The acetyl-CoA derived from amino acid degradation is normally insufficient for fatty acid biosynthesis, and the acetyl-CoA produced by pyruvate dehydrogenase and by fatty acid oxidation cannot cross the mitochondrial membrane to participate directly in fatty acid synthesis. Instead, acetyl-CoA is linked with oxaloacetate to form citrate, which is transported from the mitochondrial matrix to the cytosol by  citrate carriers (CIC),  nuclear-encoded proteins located in the mitochondrial inner membrane, members of the mitochondrial carrier family.  Biosynthesis of oxaloacetate requires malate dehydrogenase enzymes or, in plants, pyruvate carboxylase enzymes.

So all these listed functional units and substrates are required in the synthesis process. They are essential, constituting an interdependent interlocked system of the cell.

As Bruce Alberts said in 1998, the biology of the future was going to be the study of molecular machines: “the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.”  One of those machines is like a mini-factory in itself. It’s called fatty acid synthase.

The first step of fatty acid biosynthesis requires the participation of malonyl-CoA, a three-carbon intermediate.  The formation of malonyl-CoA from acetyl-CoA is an irreversible process, catalyzed by acetyl-CoA carboxylase enzymes. a multifunctional protein with 3 subunits, which is carefully regulated.

In the second step, fatty acid synthase ( FAS) proteins come into action. These are the little heroes of this article. FAS most striking feature is the “high degree of architectural complexity” – some 48 active sites, complete with moving parts

Which organism has one of the most elaborate fatty-acid machines of all?  The surprising answer: fungi. 
Perhaps the most striking feature of fungal FAS is its high degree of architectural complexity, in which 48 functional centres exist in a single ... particle.  Detailed structural information is essential for delineating how this complex particle coordinates the reactions involved in many steps of synthesis of fatty acids.... The six alpha subunits form a central wheel in the assembly, and the beta subunits form domes on the top and bottom of the wheel, creating six reaction chambers within which each Acyl Carrier Protein (ACP) can reach the six active sites through surprisingly modest movements.

The crystal structure of yeast FAS reveals that this large, macromolecular assembly functions as a six-chambered reactor for fatty acid synthesis.  Each of the six chambers functions independently and has in its chamber wall all of the catalytic units required for fatty acid priming, elongation, and termination, while one substrate-shuttling component, ACP, is located inside each chamber and functions like a swinging arm.  Surprisingly, however, the step at which the reactor is activated must occur before the complete assembly of the particle since the PPT domain that attaches the pantetheine arm to ACP lies outside the assembly, inaccessible to ACP that lies inside.  Remarkably, the architectural complexity of the FAS particle results in the simplicity of the reaction mechanisms for fatty acid synthesis in fungi.

To imagine this level of precision and master-controlled processing on a level this small, cannot help but induce a profound sense of wonder and awe.  Here, all this time, this machine has been helping to keep living things functioning and we didn’t even know the details till now.

The fatty acids are useless without the amino acids, and vice versa .  Even if some kind of metabolic cycle were to be envisioned under semi-realistic conditions, how did this elaborate machine, composed of amino acids with precise charge distributions, arise?  It’s not just the machine, it’s the blueprints and construction process that must be explained.  What blind process led to the precise placement of active sites that process their inputs in a programmed sequence?  What put them into a structure with shared walls where six reaction chambers can work independently?  All this complexity, involving thousands of precision amino acids in FAS  has to be coded in DNA, then built by the formidably complex translation process, then assembled together in the right order, or FAS won’t work.  But the storage, retrieval, translation and construction systems all need the fatty acids, too, or they won’t work.

We are witnessing an interdependent system of mind-boggling complexity that defies any explanation besides intelligent design.  Yes, Bruce Alberts, “as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered.”  We have tended to “vastly underestimate the sophistication of many of these remarkable devices.”

The closer they look, the more wondrous the cell gets.  Who would have thought that the requirement to make these fatty acids would require machinery with moving parts and reaction chambers?  Who would have imagined their surfaces would be covered with complex proteins that regulate the production inside?  Who would have realized that fat was so important, the cell had complex assembly plants to build it?  Fat is almost a mild cuss word in our vocabulary, but it is another class of molecular building blocks we couldn’t live without.  Fats, sugars, proteins and nucleic acids all work together in life, from humans to lowly fungi.  Each class of molecules has immense variety, each is essential, and each is manufactured to spec by precision machinery.  What a wonderful post-Darwinian world.

How do the origin of life researchers envision the rise of these hypercomplex nano-factories and assembly lines to make fatty acids? The scientific paper The lipid world says :

Self-assembly of amphiphilic molecules into complex supramolecular structures is spontaneous. The plausibility that such structures were present in the prebiotic environment is supported by the occurrence of amphiphilic molecules in carbonaceous meteorites and the demonstration that they can assemble into membrane vesicles


 Following parts are involved direct or indirectly in fatty acid synthesis, and must exist in order for fatty acids to be able to be synthesized :

the cytosol
NADPH.

enzymes of the Pentose phosphate pathway:

Glucose-6-phosphate dehydrogenase
6-phosphogluconolactonase
Phosphogluconate dehydrogenase
Ribose-5-phosphate isomerase
Phosphopentose epimerase
Transketolase
Transaldolase

of the glycolysis pathway, at least : hexokinase enzymes

oxaloacetate
phophopantetheinyl transferases
citrate
mitochondria
The citrate carrier (CiC)
the nucleus
malate dehydrogenase enzymes or pyruvate carboxylase enzymes
acetyl-CoA carboxylase enzymes
Acyl Carrier Proteins
FAS fatty acid synthase proteins
The citric acid cycle
ATP

This paper shows the helplessness of proponents of natural prebiotic origin of lipids. It's a huge gap between the above explanation, and the arising of hypercomplex multi enzymatic proteins, which produce fatty acids through advanced, regulated, precise, coordinated multistep factory assembly-line like robotic procedures. 

I conclude that the make of essential fatty acids, ingredients of cell membranes, requires interdependent irreducible complex procedures,  several different metabolic pathways in order to make the substrates and produce the energy used in the process, several enzymes, the whole machinery to make the assembly proteins and enzymes. Since this constitutes a complex interlocked process, it could not be due to step by step evolutionary manner. Fatty acids, constituents of the cell membranes, had to exist right from the start for life to arise. This fact makes the design inference the most rational one. Once it's granted that a series of other cell parts had to be present and were indispensable in order for the cell to be able to synthesize fatty acids, parts which I all listed, its clear evidence that a designer is the best explanation. How do you suggest would these parts form independently, initially without function, because by their own, there is no function for them, to then by magic start interacting and become interdependent and starting working in a factory like manner, producing fatty acids? To worsen the situation, the cell membrane is required in order for these procedures to be able to happen. So in order to make fatty acids, a cell membrane is required. The cell membrane, however, is made of fatty acids. That's a catch22 situation.

the reactions of this post at Facebook:

Quite funny though, to state that life started out complex because you can't imagine how such an immense organism can manifest after billions of years. Evolution gives us our best answer because all evidence agrees with it so far, & there's no evidence of this intelligent being you speak of.

Sic Transit Another fine case of 'God must have done it' based solely on personal lack of ability to find a better answer. Well done on attempting to intellectualise it, though.

Francis Mcelroy You might have had more people read your source if it didn't end in .heavenforum.org which might as well been called fairiesexist.org (fairies exist, not fairie sexist)

Bastian Soijer I've never seen any evidence for creationism. Screw peer reviews, give me reproducable facts.

Bastian Soijer And no. The fact you can't explain it, therefor god is not evidence, it is conjecture.

Anders Morell When it concerns lipids I don't know much about it. That said, the complexity of the cell is there and an it is fully possible for its intermidiet steps to find solutions by binding new chemicals and structures, the samples that didn't are not seen today.

We might never find the answer on how the first exakt process looked like as that evidence might have simply been consumed by organisms or destroyed by other factors, I can only return the comment;

It is you who have the extrodinary claim about a designer and who should provide a model for the designer testable against observation.

Hans Rehder Complexity is not an argument for intelligent design. When insufficient knowledge or understanding prompts a "god" answer, you abrogate reason.

Richard Winkler All your arguments equal I cant explain it, the unexplainable = god

Duncan Lundie It even has a name, "Argument from personal incredulity" And Grasso, I've seen and heard your "evidence" and it's a pile of shite

Jj Madruga That was too much reading. Angelo Grasso in your post are you saying Life is too complex for us to understand so there for God Must have created Life. Was that the point?

Errie Berrie ...the fuck was that?

Troy Lawrence Excellent post. And to think Darwin and the other notable forefathers of evolution thought the first single celled organism only had to crystallize amino acids to form like a snowflake crystaliizes moisture. Wow!
What is mind boggling is the interdependence of each of the lippids, fatty acids, sugars, ADP, Proteins, enzymes, and so forth.
And even worse, there is no communicative charge between nucleotides that are attached to sugars and phosphates. Thus, evolutionists are left with all the DNA for the first life formed by random unguided chance, and not only the DNA, but also the proteins for the first life. The odds are so poor it is around 1 in 10^195 to form one protein by random chance, and there are 250-500 for each cell. And this doesn't even factor the even worse odds of forming genes for each protein. To put this in perspective, winning the lottery is 1 in 10^7.  Your excellent OP magnifies the faith required for evolutionists.
All observation reveals DNA and life come from the prior life. And that is exactly what the Bible teaches, that Life begot life.

Angelo Grasso Hans Rehder once its granted that a series of other cell parts had to be present and were indispensable in order for the cell to be able to synthesize fatty acids , parts which i all listed, its clear evidence that a designer is the best explanation. How do you suggest would these parts form independently, initially without function, because by their own, there is no function for them, to then by magic start interacting and become interdependent and starting working in a factory like manner, producing fatty acids? To worse the situation, the cell membrane is required in order for these procedures to be able to happen. So in order to make fatty acids, a cell membrane is required. The cell membrane however is made of fatty acids. Thats a catch22 situation.

Steve Risner Very nice work. ID deniers are generally naive when it comes to the inner workings of cells. And this article only speaks of one little machine.