High-speed nanotechnology Superoxide Dismutase enzymes - by evolution, or design?
https://reasonandscience.catsboard.com/t3022-superoxide-dismutase-enzymes-by-evolution-or-design
Superoxide dismutase protects us from dangerously reactive forms of oxygen
We can't live without oxygen. Our cells rely on oxygen as the final acceptor of electrons in respiration, allowing us to extract far more energy from food than would be possible without oxygen. But oxygen is also a dangerous compound. Reactive forms of oxygen, such as superoxide (oxygen with an extra electron), leak from the respiratory enzymes and wreak havoc on the cell. This superoxide can then cause mutations in DNA or attack enzymes that make amino acids and other essential molecules. This is a significant problem: one study showed that for every 10,000 electrons transferred down the respiratory pathway in Escherichia coli cells, about 3 electrons end up on superoxide instead of the proper place. To combat this potential danger, most cells make superoxide dismutase, an enzyme that detoxifies superoxide.
The science paper: On the Origin of Superoxide Dismutase: An Evolutionary Perspective of Superoxide-Mediated Redox Signaling claims:
Superoxide dismutase (SOD)maybe some of the original enzymes found in primitive life. The development of ROS-detoxifying enzymes proved necessary for primitive life to exist in an oxidative world, and one of the first of these antioxidant enzymes was known as superoxide dismutase (SOD).
Question: How could cells that use oxidative phosphorylation have survived without this essential enzyme?
The paper goes on claiming:
It is highly likely that simple proteins and enzymes evolved prior to nucleic acids, and as such were critical in establishing vital cellular processes like photosynthesis, metabolism, and replication.
My comment: How did this paper pass peer-review? How could enzymes have emerged without genetic specification?
Iron (Fe) and Sulfur (S) have been shown to self-assemble into clusters that form the catalytic basis of the oldest known enzymes
My comment: Self-assembly might be the case on rare occasions. But generally, the Fe-S cluster biogenesis pathway is conserved. The general steps of the pathway are common to all kingdoms of life. The initial stage of Fe-S cluster biogenesis is accomplished by a multimeric protein complex. This is another example where Natural selection would fail. It would not have the foresight to select and produce scaffold proteins making components ( Iron/Sulfur clusters) that would be useful only in the completion of that much larger protein complex ( which by itself also would only be useful in the presence of the oxidative phosphorylation pathway ) Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overall design goal. 4
The field of free radical biology originated with the discovery of superoxide dismutase (SOD) in 1969. 3
Cu/Zn superoxide dismutase is a very efficient enzyme. It carries out up to 10 million reactions per second in one human cell. 2
One out of every ten collisions between superoxide and the enzyme will lead to a reaction. This is far more than expected, since the active site covers only a small portion of the enzyme surface, and we might expect that most collisions would occur somewhere else on the surface. The shape and characteristics of the active site, however, may give some hints to this efficiency. The active site is funnel-shaped, with the copper and zinc at the base of the funnel.
The strong positive charge of the metal ions, along with two nearby positively-charged amino acids (colored blue here), serve to draw the negatively-charged superoxide (red) into the funnel.
Dismutation
As you might guess from its name, SOD dismutes superoxide. Dismutation is a term that refers to a special type of reaction, where two equal but opposite reactions occur on two separate molecules. SOD takes two molecules of superoxide, strips the extra electron off of one, and places it on the other. So, one ends up with an electron less, forming normal oxygen, and the other ends up with an extra electron. The one with the extra electron then rapidly picks up two hydrogen ions to form hydrogen peroxide. Of course, hydrogen peroxide is also a dangerous compound, so the cell must use the enzyme catalase to detoxify it. 1
1. https://pdb101.rcsb.org/motm/94
2. https://sci-hub.yncjkj.com/10.1007/978-3-319-56372-5_8
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745492/
4. https://reasonandscience.catsboard.com/t2285-iron-sulfur-clusters-basic-building-blocks-for-life
https://reasonandscience.catsboard.com/t3022-superoxide-dismutase-enzymes-by-evolution-or-design
Superoxide dismutase protects us from dangerously reactive forms of oxygen
We can't live without oxygen. Our cells rely on oxygen as the final acceptor of electrons in respiration, allowing us to extract far more energy from food than would be possible without oxygen. But oxygen is also a dangerous compound. Reactive forms of oxygen, such as superoxide (oxygen with an extra electron), leak from the respiratory enzymes and wreak havoc on the cell. This superoxide can then cause mutations in DNA or attack enzymes that make amino acids and other essential molecules. This is a significant problem: one study showed that for every 10,000 electrons transferred down the respiratory pathway in Escherichia coli cells, about 3 electrons end up on superoxide instead of the proper place. To combat this potential danger, most cells make superoxide dismutase, an enzyme that detoxifies superoxide.
The science paper: On the Origin of Superoxide Dismutase: An Evolutionary Perspective of Superoxide-Mediated Redox Signaling claims:
Superoxide dismutase (SOD)maybe some of the original enzymes found in primitive life. The development of ROS-detoxifying enzymes proved necessary for primitive life to exist in an oxidative world, and one of the first of these antioxidant enzymes was known as superoxide dismutase (SOD).
Question: How could cells that use oxidative phosphorylation have survived without this essential enzyme?
The paper goes on claiming:
It is highly likely that simple proteins and enzymes evolved prior to nucleic acids, and as such were critical in establishing vital cellular processes like photosynthesis, metabolism, and replication.
My comment: How did this paper pass peer-review? How could enzymes have emerged without genetic specification?
Iron (Fe) and Sulfur (S) have been shown to self-assemble into clusters that form the catalytic basis of the oldest known enzymes
My comment: Self-assembly might be the case on rare occasions. But generally, the Fe-S cluster biogenesis pathway is conserved. The general steps of the pathway are common to all kingdoms of life. The initial stage of Fe-S cluster biogenesis is accomplished by a multimeric protein complex. This is another example where Natural selection would fail. It would not have the foresight to select and produce scaffold proteins making components ( Iron/Sulfur clusters) that would be useful only in the completion of that much larger protein complex ( which by itself also would only be useful in the presence of the oxidative phosphorylation pathway ) Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overall design goal. 4
The field of free radical biology originated with the discovery of superoxide dismutase (SOD) in 1969. 3
Cu/Zn superoxide dismutase is a very efficient enzyme. It carries out up to 10 million reactions per second in one human cell. 2
One out of every ten collisions between superoxide and the enzyme will lead to a reaction. This is far more than expected, since the active site covers only a small portion of the enzyme surface, and we might expect that most collisions would occur somewhere else on the surface. The shape and characteristics of the active site, however, may give some hints to this efficiency. The active site is funnel-shaped, with the copper and zinc at the base of the funnel.
The strong positive charge of the metal ions, along with two nearby positively-charged amino acids (colored blue here), serve to draw the negatively-charged superoxide (red) into the funnel.
Dismutation
As you might guess from its name, SOD dismutes superoxide. Dismutation is a term that refers to a special type of reaction, where two equal but opposite reactions occur on two separate molecules. SOD takes two molecules of superoxide, strips the extra electron off of one, and places it on the other. So, one ends up with an electron less, forming normal oxygen, and the other ends up with an extra electron. The one with the extra electron then rapidly picks up two hydrogen ions to form hydrogen peroxide. Of course, hydrogen peroxide is also a dangerous compound, so the cell must use the enzyme catalase to detoxify it. 1
1. https://pdb101.rcsb.org/motm/94
2. https://sci-hub.yncjkj.com/10.1007/978-3-319-56372-5_8
3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745492/
4. https://reasonandscience.catsboard.com/t2285-iron-sulfur-clusters-basic-building-blocks-for-life
