Cells and proteins need to be organized on an atomic scale
https://reasonandscience.catsboard.com/t3308-cells-and-proteins-need-to-be-organized-on-an-atomic-scale
Proteins and cells are the building blocks of life, and their proper organization is essential for the proper functioning of all biological systems. This organization occurs not only on the molecular scale but also on the atomic scale.
Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. The precise folding of a protein is critical for its function, and any deviation from the correct conformation can result in a loss of function or even a disease state. The folding of a protein is determined by the interactions between its constituent atoms, and even small changes in the positioning of these atoms can lead to large differences in the final structure.
In addition to the proper folding of individual proteins, the organization of proteins within cells is also critical. Cells contain a wide variety of different proteins, each with their own specific functions. These proteins must be organized spatially within the cell to allow for the efficient performance of their functions. This organization is achieved through a variety of mechanisms, including the formation of protein complexes, the localization of proteins to specific organelles, and the clustering of proteins on the cell membrane.
The precise organization of proteins within cells is also critical for the proper functioning of larger-scale biological systems, such as tissues and organs. For example, the correct organization of proteins within the extracellular matrix is critical for the proper development and function of tissues such as bone, cartilage, and skin.
Overall, the precise spatial organization of proteins and cells is essential for the proper functioning of all biological systems, from the molecular to the macroscopic scale. Achieving this organization requires a deep understanding of the interactions between atoms and molecules, as well as the complex processes that occur within cells and tissues.
The cell is able to organize and orchestrate the selection and position of atoms in each molecule, proteins, and the cell through a variety of mechanisms, including genetic regulation, molecular signaling pathways, and cellular trafficking and sorting.
Genetic regulation: The genetic information encoded in DNA provides the blueprint for the production of all the proteins and molecules within a cell. The specific sequence of DNA determines the sequence of amino acids in a protein, which in turn determines its final structure and function. Cells are able to regulate gene expression through a variety of mechanisms, including epigenetic modifications, transcription factors, and RNA processing, which help to ensure that the correct proteins are produced in the correct amounts at the correct time.
Molecular signaling pathways: Cells use a variety of signaling pathways to communicate with each other and respond to changes in their environment. These pathways involve the binding of signaling molecules to specific receptors on the surface of the cell, which triggers a series of downstream signaling events that ultimately lead to changes in gene expression, protein activity, and cellular behavior. These signaling pathways help to ensure that cells are able to respond appropriately to external stimuli and maintain homeostasis.
Cellular trafficking and sorting: Once proteins are produced within the cell, they must be sorted and transported to the correct location within the cell or secreted outside of the cell. This process is mediated by a complex network of trafficking and sorting pathways, which involve the packaging of proteins into specific vesicles, the movement of these vesicles along microtubules and actin filaments, and the fusion of these vesicles with specific organelles or the plasma membrane. These pathways help to ensure that proteins are delivered to the correct location within the cell and that they are able to perform their specific functions.
Overall, the cell is able to organize and orchestrate the selection and position of atoms in each molecule, protein, and the cell through a complex network of genetic, signaling, and trafficking pathways. This allows cells to maintain their internal organization and respond to changes in their environment, ultimately allowing them to perform their specific functions and contribute to the overall functioning of biological systems.
Aspartate Carbamoyltransferase
David Goodsell, Our Molecular Nature, page 26
Dozens of enzymes are needed to make the DNA bases cytosine and thymine from their component atoms. The second step is performed by aspartate carbamoyltransferase. In bacteria, this enzyme controls the entire pathway. (In human cells, the regulation is more complex, involving the interaction of several of the enzymes in the pathway.) The enzyme is composed of six large catalytic subunits and six smaller regulatory subunits . The active site of the enzyme is located where two individual catalytic subunits touch, so the position of the two subunits relative to one another is critical. Take just a moment to ponder the immensity of this enzyme. The entire complex is composed of over 40,000 atoms, each of which plays a vital role. The handful of atoms that actually perform the chemical reaction are the central players. But they are not the only important atoms within the enzyme--every atom plays a supporting pan. The atoms lining the surfaces between subunits are chosen to complement one another exactly, to orchestrate the shifting regulatory motions. The atoms covering the surface are carefully picked to interact optimally with water, ensuring that the enzyme doesn't form a pasty aggregate, but remains an individual, floating factory. And the thousands of interior atoms are chosen to fit like a jigsaw puzzle, interlocking into a sturdy framework. Aspartate carbamoyltransferase is fully as complex as any fine automobile in our familiar world.
The ribosome
The precise order of atoms in the ribosome is critical for its functioning. The structure of the ribosome is essential for its function, and any disruption to this structure can have a profound effect on its ability to function properly. In particular, the precise order of atoms in the ribosome is crucial for the formation of the active site where the peptide bond formation occurs during protein synthesis. Any alteration or disruption of the atomic order in the ribosome can affect its ability to correctly read and interpret the genetic code and can lead to errors in protein synthesis. Thus, the precise order of atoms is critical for the ribosome's function.
A2451 is a specific nucleotide residue within the ribosome's large subunit rRNA (23S rRNA) that plays a crucial role in the peptidyl transferase activity of the ribosome. It is located in the ribosome's active site, which is responsible for catalyzing the formation of peptide bonds during protein synthesis.
A2451 is positioned adjacent to the aminoacyl-tRNA substrate and acts as a critical base for the deprotonation of the amino group of the aminoacyl-tRNA during the peptidyl transfer reaction. This deprotonation is necessary to activate the amino group for nucleophilic attack on the carbonyl carbon of the peptidyl-tRNA in the A-site, which leads to the formation of a peptide bond between the two amino acids.
Moreover, A2451 has been shown to be important for the accuracy of protein synthesis by the ribosome. Mutations or modifications that alter A2451 have been found to affect the fidelity of translation and can lead to the incorporation of incorrect amino acids into the growing protein chain. If A2451 were not in the correct position or were missing altogether, it would likely prevent the proper deprotonation of the amino group, thereby hindering the formation of peptide bonds during protein synthesis. This, in turn, would lead to incomplete or incorrect protein synthesis and could have significant implications for cellular function and overall health. The odds of finding the precise location for A2451 in the ribosome are extremely low. The ribosome is a large and complex molecular machine, consisting of over 50 proteins and three RNA molecules, and the location of A2451 within the ribosome's active site is critical for its function in protein synthesis.
The right hydrogen bonds for Watson-Crick base-pairing
The isomeric arrangement of nucleobases and the atomic selection are critical for the formation of stable Watson-Crick base pairs, which are the foundation of the genetic code and the transmission of genetic information in living organisms. The hydrogen bonding between complementary nucleobases is a key determinant of the stability of the double-stranded DNA molecule, and any deviation from the precise atomic arrangement required for hydrogen bonding could lead to disruptions in base-pairing and potential errors in genetic information.
For example, certain isomers of nucleobases, such as the tautomeric form of cytosine, can disrupt hydrogen bonding between base pairs, leading to the formation of mismatched or unstable base pairs. These mismatches can lead to errors in DNA replication and transcription, which can ultimately affect the proper functioning of cells and biological systems. Similarly, if the atomic selection of nucleobases is not correct, it can lead to changes in the hydrogen bonding strength between complementary base pairs, which can affect the stability of the DNA molecule and its ability to transmit genetic information accurately.
It is thought that the formation of stable Watson-Crick base pairs played a critical role in the emergence of life, as it allowed for the accurate transmission and replication of genetic information.
More examples
Following are some additional examples of how fine-tuning the bond strengths through precise atomic and molecular arrangements is essential for proper functioning in biological systems, including on an epigenetic level:
Histone modifications: Histones are proteins that play a critical role in packaging DNA in the nucleus of cells. Post-translational modifications of histones, such as acetylation, methylation, and phosphorylation, can alter the charge and conformation of the histone protein, affecting the strength of the interactions between histones and DNA. These modifications can also serve as binding sites for proteins that regulate gene expression, and can ultimately affect the transcription and translation of genes.
Protein-protein interactions: Many cellular processes rely on the precise interactions between proteins, which are often mediated by non-covalent interactions, such as hydrogen bonding and van der Waals interactions. The strength and specificity of these interactions are dependent on the precise arrangement of atoms and molecules in the proteins, and deviations from the correct arrangement can lead to improper functioning or even protein misfolding and aggregation.
RNA splicing: RNA splicing is a process by which pre-mRNA molecules are edited to remove introns and join exons, ultimately producing mature mRNA molecules that can be translated into proteins. This process is mediated by a large complex of proteins and RNA molecules, and is highly dependent on the precise molecular arrangements of these components. Any deviations from the correct molecular arrangement can lead to improper splicing and the production of dysfunctional proteins.
Information is key
Information is a key factor in the precise organization of molecules, proteins, and cells. The genetic information encoded in DNA provides the blueprint for the production of all the proteins and molecules within a cell, and cells are able to regulate gene expression and protein production to ensure that the correct proteins are produced in the correct amounts at the correct time. Additionally, cells use a variety of signaling pathways to communicate with each other and respond to changes in their environment, which allows them to maintain their internal organization and respond to external stimuli. Cellular trafficking and sorting pathways also rely on specific information encoded in proteins and lipids to ensure that molecules are delivered to the correct location within the cell or secreted outside of the cell.
Overall, the precise organization of molecules, proteins, and cells requires a deep understanding of the information encoded within DNA and the complex signaling and trafficking pathways that allow cells to interpret and respond to this information. This information is critical for the proper functioning of biological systems at all scales, from the molecular to the macroscopic.
Epigenetic information
Epigenetic codes and information also play a critical role in the spatial organization of atoms in cells. Epigenetic information refers to heritable changes in gene expression that occur without changes to the underlying DNA sequence. These changes can occur through a variety of mechanisms, including modifications to DNA and histone proteins, which can affect how genes are packaged and expressed within the cell.
One of the key ways that epigenetic information affects the spatial organization of atoms in cells is through the regulation of gene expression. Epigenetic modifications can alter the accessibility of DNA to transcription factors and other regulatory proteins, which can affect the production of specific proteins and molecules within the cell. For example, modifications to histone proteins can affect the folding of DNA and the accessibility of specific genes, which can ultimately affect the production of proteins that are critical for the proper organization and functioning of cells.
Epigenetic information can also affect the trafficking and sorting of proteins within cells. For example, modifications to specific proteins or lipids can alter their interactions with trafficking and sorting machinery, which can affect their delivery to specific locations within the cell. Additionally, changes in epigenetic information can affect the production of specific signaling molecules, which can ultimately affect how cells communicate and respond to their environment.
Conclusion
Information, as seen in cells, has never been seen to emerge and arise by spontaneous, unguided events. The emergence of systems that contain, convey, transmit, and use complex instructional information requires intelligent input and design. The fact that cells require the precise, correct arrangement of atoms in the right order, and the right place, directed by instructional information, stored in genetic, and epigenetic systems, is clear evidence of intelligent design.
Atomic Biology vs. Evolution - Darwin's Replacement - Life by Super-Intelligence, Not Evolution
https://www.youtube.com/watch?v=Y4Qok6ujjAE
https://reasonandscience.catsboard.com/t3308-cells-and-proteins-need-to-be-organized-on-an-atomic-scale
Proteins and cells are the building blocks of life, and their proper organization is essential for the proper functioning of all biological systems. This organization occurs not only on the molecular scale but also on the atomic scale.
Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. The precise folding of a protein is critical for its function, and any deviation from the correct conformation can result in a loss of function or even a disease state. The folding of a protein is determined by the interactions between its constituent atoms, and even small changes in the positioning of these atoms can lead to large differences in the final structure.
In addition to the proper folding of individual proteins, the organization of proteins within cells is also critical. Cells contain a wide variety of different proteins, each with their own specific functions. These proteins must be organized spatially within the cell to allow for the efficient performance of their functions. This organization is achieved through a variety of mechanisms, including the formation of protein complexes, the localization of proteins to specific organelles, and the clustering of proteins on the cell membrane.
The precise organization of proteins within cells is also critical for the proper functioning of larger-scale biological systems, such as tissues and organs. For example, the correct organization of proteins within the extracellular matrix is critical for the proper development and function of tissues such as bone, cartilage, and skin.
Overall, the precise spatial organization of proteins and cells is essential for the proper functioning of all biological systems, from the molecular to the macroscopic scale. Achieving this organization requires a deep understanding of the interactions between atoms and molecules, as well as the complex processes that occur within cells and tissues.
The cell is able to organize and orchestrate the selection and position of atoms in each molecule, proteins, and the cell through a variety of mechanisms, including genetic regulation, molecular signaling pathways, and cellular trafficking and sorting.
Genetic regulation: The genetic information encoded in DNA provides the blueprint for the production of all the proteins and molecules within a cell. The specific sequence of DNA determines the sequence of amino acids in a protein, which in turn determines its final structure and function. Cells are able to regulate gene expression through a variety of mechanisms, including epigenetic modifications, transcription factors, and RNA processing, which help to ensure that the correct proteins are produced in the correct amounts at the correct time.
Molecular signaling pathways: Cells use a variety of signaling pathways to communicate with each other and respond to changes in their environment. These pathways involve the binding of signaling molecules to specific receptors on the surface of the cell, which triggers a series of downstream signaling events that ultimately lead to changes in gene expression, protein activity, and cellular behavior. These signaling pathways help to ensure that cells are able to respond appropriately to external stimuli and maintain homeostasis.
Cellular trafficking and sorting: Once proteins are produced within the cell, they must be sorted and transported to the correct location within the cell or secreted outside of the cell. This process is mediated by a complex network of trafficking and sorting pathways, which involve the packaging of proteins into specific vesicles, the movement of these vesicles along microtubules and actin filaments, and the fusion of these vesicles with specific organelles or the plasma membrane. These pathways help to ensure that proteins are delivered to the correct location within the cell and that they are able to perform their specific functions.
Overall, the cell is able to organize and orchestrate the selection and position of atoms in each molecule, protein, and the cell through a complex network of genetic, signaling, and trafficking pathways. This allows cells to maintain their internal organization and respond to changes in their environment, ultimately allowing them to perform their specific functions and contribute to the overall functioning of biological systems.
Aspartate Carbamoyltransferase
David Goodsell, Our Molecular Nature, page 26
Dozens of enzymes are needed to make the DNA bases cytosine and thymine from their component atoms. The second step is performed by aspartate carbamoyltransferase. In bacteria, this enzyme controls the entire pathway. (In human cells, the regulation is more complex, involving the interaction of several of the enzymes in the pathway.) The enzyme is composed of six large catalytic subunits and six smaller regulatory subunits . The active site of the enzyme is located where two individual catalytic subunits touch, so the position of the two subunits relative to one another is critical. Take just a moment to ponder the immensity of this enzyme. The entire complex is composed of over 40,000 atoms, each of which plays a vital role. The handful of atoms that actually perform the chemical reaction are the central players. But they are not the only important atoms within the enzyme--every atom plays a supporting pan. The atoms lining the surfaces between subunits are chosen to complement one another exactly, to orchestrate the shifting regulatory motions. The atoms covering the surface are carefully picked to interact optimally with water, ensuring that the enzyme doesn't form a pasty aggregate, but remains an individual, floating factory. And the thousands of interior atoms are chosen to fit like a jigsaw puzzle, interlocking into a sturdy framework. Aspartate carbamoyltransferase is fully as complex as any fine automobile in our familiar world.
The ribosome
The precise order of atoms in the ribosome is critical for its functioning. The structure of the ribosome is essential for its function, and any disruption to this structure can have a profound effect on its ability to function properly. In particular, the precise order of atoms in the ribosome is crucial for the formation of the active site where the peptide bond formation occurs during protein synthesis. Any alteration or disruption of the atomic order in the ribosome can affect its ability to correctly read and interpret the genetic code and can lead to errors in protein synthesis. Thus, the precise order of atoms is critical for the ribosome's function.
A2451 is a specific nucleotide residue within the ribosome's large subunit rRNA (23S rRNA) that plays a crucial role in the peptidyl transferase activity of the ribosome. It is located in the ribosome's active site, which is responsible for catalyzing the formation of peptide bonds during protein synthesis.
A2451 is positioned adjacent to the aminoacyl-tRNA substrate and acts as a critical base for the deprotonation of the amino group of the aminoacyl-tRNA during the peptidyl transfer reaction. This deprotonation is necessary to activate the amino group for nucleophilic attack on the carbonyl carbon of the peptidyl-tRNA in the A-site, which leads to the formation of a peptide bond between the two amino acids.
Moreover, A2451 has been shown to be important for the accuracy of protein synthesis by the ribosome. Mutations or modifications that alter A2451 have been found to affect the fidelity of translation and can lead to the incorporation of incorrect amino acids into the growing protein chain. If A2451 were not in the correct position or were missing altogether, it would likely prevent the proper deprotonation of the amino group, thereby hindering the formation of peptide bonds during protein synthesis. This, in turn, would lead to incomplete or incorrect protein synthesis and could have significant implications for cellular function and overall health. The odds of finding the precise location for A2451 in the ribosome are extremely low. The ribosome is a large and complex molecular machine, consisting of over 50 proteins and three RNA molecules, and the location of A2451 within the ribosome's active site is critical for its function in protein synthesis.
The right hydrogen bonds for Watson-Crick base-pairing
The isomeric arrangement of nucleobases and the atomic selection are critical for the formation of stable Watson-Crick base pairs, which are the foundation of the genetic code and the transmission of genetic information in living organisms. The hydrogen bonding between complementary nucleobases is a key determinant of the stability of the double-stranded DNA molecule, and any deviation from the precise atomic arrangement required for hydrogen bonding could lead to disruptions in base-pairing and potential errors in genetic information.
For example, certain isomers of nucleobases, such as the tautomeric form of cytosine, can disrupt hydrogen bonding between base pairs, leading to the formation of mismatched or unstable base pairs. These mismatches can lead to errors in DNA replication and transcription, which can ultimately affect the proper functioning of cells and biological systems. Similarly, if the atomic selection of nucleobases is not correct, it can lead to changes in the hydrogen bonding strength between complementary base pairs, which can affect the stability of the DNA molecule and its ability to transmit genetic information accurately.
It is thought that the formation of stable Watson-Crick base pairs played a critical role in the emergence of life, as it allowed for the accurate transmission and replication of genetic information.
More examples
Following are some additional examples of how fine-tuning the bond strengths through precise atomic and molecular arrangements is essential for proper functioning in biological systems, including on an epigenetic level:
Histone modifications: Histones are proteins that play a critical role in packaging DNA in the nucleus of cells. Post-translational modifications of histones, such as acetylation, methylation, and phosphorylation, can alter the charge and conformation of the histone protein, affecting the strength of the interactions between histones and DNA. These modifications can also serve as binding sites for proteins that regulate gene expression, and can ultimately affect the transcription and translation of genes.
Protein-protein interactions: Many cellular processes rely on the precise interactions between proteins, which are often mediated by non-covalent interactions, such as hydrogen bonding and van der Waals interactions. The strength and specificity of these interactions are dependent on the precise arrangement of atoms and molecules in the proteins, and deviations from the correct arrangement can lead to improper functioning or even protein misfolding and aggregation.
RNA splicing: RNA splicing is a process by which pre-mRNA molecules are edited to remove introns and join exons, ultimately producing mature mRNA molecules that can be translated into proteins. This process is mediated by a large complex of proteins and RNA molecules, and is highly dependent on the precise molecular arrangements of these components. Any deviations from the correct molecular arrangement can lead to improper splicing and the production of dysfunctional proteins.
Information is key
Information is a key factor in the precise organization of molecules, proteins, and cells. The genetic information encoded in DNA provides the blueprint for the production of all the proteins and molecules within a cell, and cells are able to regulate gene expression and protein production to ensure that the correct proteins are produced in the correct amounts at the correct time. Additionally, cells use a variety of signaling pathways to communicate with each other and respond to changes in their environment, which allows them to maintain their internal organization and respond to external stimuli. Cellular trafficking and sorting pathways also rely on specific information encoded in proteins and lipids to ensure that molecules are delivered to the correct location within the cell or secreted outside of the cell.
Overall, the precise organization of molecules, proteins, and cells requires a deep understanding of the information encoded within DNA and the complex signaling and trafficking pathways that allow cells to interpret and respond to this information. This information is critical for the proper functioning of biological systems at all scales, from the molecular to the macroscopic.
Epigenetic information
Epigenetic codes and information also play a critical role in the spatial organization of atoms in cells. Epigenetic information refers to heritable changes in gene expression that occur without changes to the underlying DNA sequence. These changes can occur through a variety of mechanisms, including modifications to DNA and histone proteins, which can affect how genes are packaged and expressed within the cell.
One of the key ways that epigenetic information affects the spatial organization of atoms in cells is through the regulation of gene expression. Epigenetic modifications can alter the accessibility of DNA to transcription factors and other regulatory proteins, which can affect the production of specific proteins and molecules within the cell. For example, modifications to histone proteins can affect the folding of DNA and the accessibility of specific genes, which can ultimately affect the production of proteins that are critical for the proper organization and functioning of cells.
Epigenetic information can also affect the trafficking and sorting of proteins within cells. For example, modifications to specific proteins or lipids can alter their interactions with trafficking and sorting machinery, which can affect their delivery to specific locations within the cell. Additionally, changes in epigenetic information can affect the production of specific signaling molecules, which can ultimately affect how cells communicate and respond to their environment.
Conclusion
Information, as seen in cells, has never been seen to emerge and arise by spontaneous, unguided events. The emergence of systems that contain, convey, transmit, and use complex instructional information requires intelligent input and design. The fact that cells require the precise, correct arrangement of atoms in the right order, and the right place, directed by instructional information, stored in genetic, and epigenetic systems, is clear evidence of intelligent design.
Atomic Biology vs. Evolution - Darwin's Replacement - Life by Super-Intelligence, Not Evolution
https://www.youtube.com/watch?v=Y4Qok6ujjAE
Last edited by Otangelo on Thu Aug 03, 2023 11:48 am; edited 2 times in total