The amazing fatty acid synthase nano factories, and origin of life scenarios
Post Reply
 
Thread Rating:
  • 0 Votes - 0 Average
  • 1
  • 2
  • 3
  • 4
  • 5
28-08-2015, 08:54 AM
The amazing fatty acid synthase nano factories, and origin of life scenarios
The amazing fatty acid synthase nano factories, and origin of life scenarios

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 a 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 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 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 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.

How do origin of life researchers envision the arise of these hyper complex 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.

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 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 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.

http://reasonandscience.heavenforum.org/...-scenarios

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 enzymes :

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
Find all posts by this user
Like Post Quote this message in a reply
28-08-2015, 09:06 AM
RE: The amazing fatty acid synthase nano factories, and origin of life scenarios
(28-08-2015 08:54 AM)Godexists Wrote:  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...

<snip>

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?

Argument from personal incredulity.

We're already done here, folks.

"Owl," said Rabbit shortly, "you and I have brains. The others have fluff. If there is any thinking to be done in this Forest - and when I say thinking I mean thinking - you and I must do it."
- A. A. Milne, The House at Pooh Corner
Find all posts by this user
Like Post Quote this message in a reply
[+] 2 users Like Unbeliever's post
28-08-2015, 09:30 AM
RE: The amazing fatty acid synthase nano factories, and origin of life scenarios
Too bad your stupid impotent deity is so limited that he MUST make life happen in exactly the way one might expect if it were to have evolved.

ID is an argument AGAINST the omnipotence of a god.

The next thing you know, you're gonna be trying to tell us it was the Christian god (Yahweh, the 70th son of the Babylonian chief god, El Elyon, and also the Babylonian War god, and the god who protected the armies), that did all this. Weeping

Insufferable know-it-all.Einstein God has a plan for us. Please stop screwing it up with your prayers.
Find all posts by this user
Like Post Quote this message in a reply
[+] 1 user Likes Bucky Ball's post
28-08-2015, 09:33 AM
RE: The amazing fatty acid synthase nano factories, and origin of life scenarios
Anyone done a periodicity study on GE?

I think he has a pattern of websites (all nonbeliever ones?) he goes around to, dropping this crap like a missionary handing out pamphlets before moving on to the "next house" in the Name of Jayzus™.

I think it's long since past time this guy got hammered for spamming, since he will not honestly address the flaws in his copypasta nor acknowledge when new information comes out that disproves his stuff.

He'll just get frustrated with us, leave, and go through the cycle described before returning here with fresh copypasta, like the last one wasn't decimated. I do enjoy discussing and even debating biology/ID, but I think GE has clearly progressed beyond incidental spamming and right up to the point of willful disrespect, which is my threshold for recommending the Ban Hammer.

"Theology made no provision for evolution. The biblical authors had missed the most important revelation of all! Could it be that they were not really privy to the thoughts of God?" - E. O. Wilson
Find all posts by this user
Like Post Quote this message in a reply
[+] 2 users Like RocketSurgeon76's post
28-08-2015, 09:34 AM
RE: The amazing fatty acid synthase nano factories, and origin of life scenarios
(28-08-2015 08:54 AM)Godexists Wrote:  The amazing fatty acid synthase nano factories, and origin of life scenarios

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 a 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 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 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 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.

How do origin of life researchers envision the arise of these hyper complex 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.

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 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 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.

http://reasonandscience.heavenforum.org/...-scenarios

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 enzymes :

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

I assume you realize that I'm not going to read a word of that....
Find all posts by this user
Like Post Quote this message in a reply
28-08-2015, 09:38 AM
RE: The amazing fatty acid synthase nano factories, and origin of life scenarios
(28-08-2015 09:34 AM)Aliza Wrote:  I assume you realize that I'm not going to read a word of that....

Don't worry, you're not missing anything.

Here; I'll summarise:
1. I don't understand [insert biological copypasta here]
2. Therefore irreducible complexity
3. Therefore GAAAAAAAWD
(insulting the audience optional)

... this is my signature!
Find all posts by this user
Like Post Quote this message in a reply
[+] 5 users Like cjlr's post
28-08-2015, 09:56 AM
RE: The amazing fatty acid synthase nano factories, and origin of life scenarios
(28-08-2015 09:34 AM)Aliza Wrote:  I assume you realize that I'm not going to read a word of that....

What pisses me off about GE is that I used to sort through all that crap and actually address it, and then instead of acknowledging there's an error in his approach to ID/IC, he just comes right back with more "examples".

It's a lot of work to address, for no gain (since the answers will be ignored by the fundie), and therefore fundamentally (pun intended) dishonest.

"Theology made no provision for evolution. The biblical authors had missed the most important revelation of all! Could it be that they were not really privy to the thoughts of God?" - E. O. Wilson
Find all posts by this user
Like Post Quote this message in a reply
28-08-2015, 10:13 AM
RE: The amazing fatty acid synthase nano factories, and origin of life scenarios
[Image: FwCCJlQ.jpg]

[Image: ZF1ZJ4M.jpg]
Visit this user's website Find all posts by this user
Like Post Quote this message in a reply
[+] 5 users Like houseofcantor's post
29-08-2015, 06:40 PM
RE: The amazing fatty acid synthase nano factories, and origin of life scenarios
So nobody wants to take a stance, and actually address my arguments ??
Ahm...... actually, thats probably the best strategy in order to hide that the emperor has no cloths.


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 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.

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
Find all posts by this user
Like Post Quote this message in a reply
29-08-2015, 06:50 PM (This post was last modified: 29-08-2015 07:13 PM by GirlyMan.)
RE: The amazing fatty acid synthase nano factories, and origin of life scenarios
(29-08-2015 06:40 PM)Godexists Wrote:  So nobody wants to take a stance, and actually address my arguments ??

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?

Hell, I'll give it a go.





There is only one really serious philosophical question, and that is suicide. -Camus
Find all posts by this user
Like Post Quote this message in a reply
[+] 1 user Likes GirlyMan's post
Post Reply
Forum Jump: